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The Chain of Command

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When an organisation gets to a certain size, it becomes necessary for the higher ups to start delegating to subordinates since it becomes harder and harder for them to keep track of everything going on. It's one thing for the Big Good to issue instructions directly to the Five-Man Band when it's just a small La Résistance of a few dozen people, but that becomes unwieldy when you get to the level of The Federation and the Big Good now commands thousands or hundreds of thousands of people.
A chain of command refers to formal (or sometimes informal) ranking systems where people at the top and bottom of the chain generally don't communicate directly. Instead, if the person at the top wants something done he or she issues the command to their direct subordinate, who then passes the order down to their subordinate, who then passes down the order to their's, until it reaches the people who actually execute the task (this being akin to the links in a chain, hence the "chain" in chain of command). Similarly, someone wanting to report something would be expected to report to their direct superior, who would then pass it up to their superior up the chain until it reaches someone who can actually do something about it.
While this most often appears in Military and Warfare Works, this can be seen in just about any work that involves organisations, such as Crime Fiction (on both sides of the law), School Stories Example in real life a Class Representative would bring up student concerns to a Student Council President who'd then bring them up to their advisor, who'd then pass it up to the school administration or even businesses. A common breach of protocol can involve a subordinate bypassing their direct superior and going right to their superior (described as "going over someone's head"). Similarly, it can be considered poor form for a superior to bypass their direct subordinate to issue commands directly to the subordinate's subordinates, even if it's technically allowed. Example the President of the United States of America, in the role of Commander-In-Chief, could give orders directly to a sergeant... but considering that bypasses the entire military chain of command between the President and the sergeant it would make for a very poor look. In addition, it'd be a faux pas for an officer to give orders to the subordinates of another officer directly without consulting the other officer. The chain of command means that individual members take orders from only one superior and only give orders to a defined group of people immediately below them, in order to maintain clarity and to avoid confusion.
As far as the military is concerned, however, there are some basic rules to the chain of command (which can also apply to organisations based on the the military model like police):
In general, military personnel give orders only to those directly below them in the chain of command and receive orders only from those directly above them. E.g. a captain wouldn't directly give orders to a corporal, instead giving the orders to a lieutenant who'd then pass them to a sergeant who'd then order the corporal. Similarly, a general wouldn't give orders directly to a captain; instead the captain's orders would come from his or her direct superior like a major.
An officer is usually expected to give orders only to his or her direct subordinate(s), regardless of rank. Example Bright Noa at his rank of Lieutenant outranks Shiro Amada (a second lieutenant). However, as Shiro is a member of a completely different unit and not part of Bright's command, Bright would have to contact Shiro's superior instead. Shiro in fact could either simply obey the orders, or advise that the orders have to be cleared with his superior. If Bright insists (e.g. it's an emergency so there isn't time to go through the normal channels), Shiro would be obligated to obey (since he must presume the orders given are legitimate). But even in such a case, Shiro would also have to consider if the new orders conflict with orders given by his own superior e.g. if he'd been ordered to hold a position, and Bright orders him to instead move to reinforce a different position which would mean abandoning the place he'd been tasked with defending by his superior.
Higher rank doesn't necessarily mean higher up the chain of command, with authority also depending on one's position within a particular chain of command. This is why the G.I.Joe example below is an example of Shown Their Work, since while Duke is merely a First Sergeant, in the G.I.Joe chain of command he's the field commander and so outranks people who'd outrank him normally.
There are, naturally, problems with a chain of command. The longer the chain, the more time it takes for orders and reports to go up and down the chain, resulting in a slowed reaction time. An Obstructive Bureaucrat or two can add to the slowed reaction time, especially if they're sticklers for protocol. Right Hand Versus Left Hand can come about because the people lower down the chain don't know what others are doing and so accidentally get in each others' way. The Peter Principle occurs when someone is promoted up the chain beyond their ability to perform, thus also affecting the smooth running of the organisation. Jurisdiction Friction and Interservice Rivalry can also result (especially when a particular unit or group is placed outside the regular chain of command, breeding resentment), as well as a Delegation Relay when people don't want do deal with something and so use the chain of command to pass the buck (either upwards or downwards). Part of the reason a Bavarian Fire Drill can work is when people are so accustomed to following a chain of command they forget a crucial step (which is to confirm the person giving orders is actually authorised to do so). And that's before getting into the possibilities of The Mole or worse a Mole in Charge.
Expect to see this in media involving a Command Roster or The Squad, while Mildly Military works might at least pay lip service. Repeat to Confirm is one way the chain of command can be shown as moving smoothly, as it makes sure there's no ambiguity about orders coming down. That's an Order! and That Wasn't a Request are two ways how orders can be delivered via the chain of command (the former being more formal than the latter). This trope is also why Straight for the Commander and Decapitated Army exist, since even if the opposing force isn't a Keystone Army the disruption that comes about from reestablishing the chain of command opens opportunities that can be exploited. You Are in Command Now, Field Promotion even Closest Thing We Got are scenarios that can happen when the regular chain of command is disrupted or broken, forcing people to repair the chain or form a new one as best they can. Inappropriately Close Comrades can be Played for Drama specifically because of fears of disruption to the chain of command.
Not to be confused with The Chains of Commanding, which can overlap with this due to that trope being about how being higher up the chain can lead to much heavier mental stress. Also nothing to do with Slave Collar (which was formerly named Chain Of Command).

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Mobile Suit Zeta Gundam: Part of the reason the Anti-Earth Union Group (AEUG) is formed and includes many members and ex-members of the Earth Federation military is because the Titans were formed and deliberately placed outside the military chain of command, yet given authority over the regular military. As an example, Jerid Mesa (a mere Lieutenant Junior Grade) is able to physically assault war hero Bright Noa (who at the rank of Commander is three ranks above him) with impunity simply because Jerid was a Titan and Bright wasn't. The Titans also abuse their authority by using regular Federal troops as Cannon Fodder.
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Starcraft: When Terran units are grouped together, the units are arranged in order of rank, with the highest ranks going first. While ranks are just a cosmetic rating, more powerful units are higher ranking and so will be listed first. For example, if gathering a mixed force, you'd have Goliaths (First Sergeant) followed by Siege tanks (Master Sergeant) followed by Vultures (Sergeant), then Firebats (Corporal) and finally the Marines (Private). On the other hand, heroes will always go first, no matter their rank e.g. Sarah Kerrigan (Lieutenant) will be listed ahead of units like Wraiths (Captain) or Battlecruisers (Commodore). This is ditched in Starcraft II, where units that have more and frequently-used abilities are prioritized first, and ranks are determined by kills instead.
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CSI: NY: Discussed in "Officer Blue." One suspect had been dishonorably discharged from the Army because he went against orders from his commanding officer. Mac takes much offense from this and tells the man that, as a Marine, he knows the chain of command is sacrosanct.
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In Command & Conquer 3: Tiberium Wars, GDI's chain of command results in a hasty reassignment of leadership after the Philadelphia space station is destroyed at the start of the game, much of GDI's higher-ups with them as they were attending an energy summit at the time. Secretary of the Treasury Redmond Boyle is made acting director, who often thinks more about publicity and makes rash decisions for GDI. In Kane's Wrath it's revealed that this is exploited by none other than Kane, who was counting on Boyle's hot-headedness to advance his own agenda.
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Master and Commander: The midshipman Mr Hollom is nigh universally disliked by his crewmates, with even Captain Aubery having a certain amount of contempt for him. The seamen dislike him because of his indecisive demeanor (not helped by his pathetically transparent attempts to bond with the crew members), while Aubery dislikes him because those same flaws means he has few to no leadership qualities and so jeopardizes the chain of command note  A midshipman of that era was roughly equivalent to a modern petty officer or sergeant, making them the link between the officers and the rank-and-file crew. His fears come to pass when one of the crew deliberately bumps into Hollom and walks off, prompting the enraged captain to have the man locked up. He also summons Hollom to his cabin to dress him down for not taking any action himself, since by permitting such a blatant and public show of insolence to go unpunished he jeopardized the crew's discipline. Aubery later has the offender who bumped into Hollom flogged for insubordination.
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G.I. Joe: A Real American Hero
"Arise, Serpentor, Arise! Part One" has Beach Head complaining to General Hawk, Duke and Flint that they're letting the Joes get soft, going so far as to begin saying, "If I were in charge..." only to be cut off by Flint reminding him of the actual Joe chain of command: General Hawk, Duke, Flint and then Beach Head.
In the episode "The Most Dangerous Thing in the World", COBRA's plan revolves around disrupting the Joe chain of command while their leaders General Hawk, Duke and Flint are away by promoting Dial Tone, Lifeline and Shipwreck to the rank of colonel (despite Shipwreck being from the Navy). As COBRA hoped, Joe morale plummets due to the three's idiosyncracies note  for example, a training session almost goes disastrously wrong when Dial Tone rewires some inert missiles to perform a BoomerangComeback as a safety feature, Shipwreck (not knowing about the modifications) decides to use said missiles and rearms them to make it a live fire exercise, and unknown to both Lifeline had the weapons on the vehicles participating in the exercise disabled for "safety reasons". So the Joes aren't able to shoot down the missiles like they're supposed to, and when they drive their vehicles behind cover there's a Mass "Oh, Crap!" when the missiles turn back and strike the vehicles from behind, the Joes participating barely able to get out in time before they explode. A COBRA attack on the Joe HQ almost succeeds until General Hawk arrives to take personal command.
When the bogus orders come in, Mainframe contacts the Department of Defense twice but gets an affirmative both times. That's when he calls in Beach Head, the ranking officer present on-base. Despite his confusion (pointing out Shipwreck isn't even in the Army) Beach Head complies with the orders... but also has Mainframe try to get in touch with General Hawk, leading to Hawk's Big Damn Heroes arrival.
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In Combat Kelly and his Deadly Dozen #4, Sergeant Nick Fury assumes command when Captain Conner (who was meant to command the Allied troops bracing for an Axis assault) is paralyzed with fear. Kelly points out that as an NCO, Fury doesn't have the right to do so but Fury retorts that since the battle has already begun there isn't time to find an officer to take Conner's place.
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Star Trek: Discovery: One of the complaints about the series is how there is blatant disrespect for the chain of command, with crewmen often talking back to or snarking at their superior officers. Even taking into account the Mildly Military nature of Starfleet, such unprofessional behaviour was so blatant that it broke Willing Suspension of Disbelief.
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G.I. Joe. G.I.Joe's A Real American Hero characters all have a military rank (barring a few outliers), something Larry Hama paid close attention to when he was developing the characters. However, the chain of command in G.I.Joe differs from the actual ranks the characters have, partially because the Joe team is a combined unit with members from various branches of the military serving under the same chain of command.
General Hawk is ranked O-7 (Brigadier General) and the one in command of the Joe team as a whole. However, the field commander is Duke with a rank of E-8 (First Sergeant). Duke is explicitly higher up the Joe chain of command than Flint (W-2, Chief Warrant Officer), Cutter (O-2, Lieutenant Junior Grade), and Doc and Ace (both O-3, Captain), all of whom outrank him according to their branches. Shipwreck (E-7, Chief Petty Officer) isn't even in the chain of command while Beach Head (E-6, Staff Sergeant) is.
Since COBRA is a terrorist organisation their filecards instead mention the closest estimated equivalent. For example, the Crimson Guard's filecard gives them a rank of E-4 (or equivalent), while Cobra Commander's grade is simply given as Commander-In-Chief. A few COBRA aligned characters who are technically outside consultants like Firefly, Wild Weasel and even Destro don't have ranks. note  It should also be pointed out that in the case of the Crimson Guard, this is actually Fridge Brilliance: the rank on their filecard simply gives their estimated rank, and the Crimson Guard when seen in combat appear to simply be frontline sergeants. The Joes are unaware that their real role is to infiltrate society and work their way up to positions of power where they can quietly aid COBRA's goals with no one being the wiser. Some filecards even note that a single Crimson Guardsman who is a trusted aide to a Senator can do much more damage to the Joes than an entire tank platoon... all with the swish of a pen.
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Margin Call provides a very stark business example of the chain of command. Before the 2008 credit collapse, Peter Sullivan, a junior risk analyst at a major investment bank discovers a problem with their main investment products that could cause the firm to become insolvent in a single trading day if people started panic selling. He reports this to his boss's boss (his original boss, senior analyst Eric Dale, was fired earlier that day), a senior trader, who reports this to his boss, the trading floor manager, who reports this to his bosses, the division chief and the chief risk management officer, before finally bringing in the CEO for an emergency meeting with all the partners.
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The Transformers: Whenever the Autobots are shown preparing to mobilise (especially in the "More Than Meets The Eye" miniseries that began the series), Optimus Prime issues the orders to his lieutenant Jazz, who then assembles the Autobots and informs Optimus when they're ready. In the final part of the miniseries the Autobots prepare to launch a Death or Glory Attack on the Decepticon encampment. Optimus Prime gives a Rousing Speech to the Autobots (and their human allies Spike and Sparkplug) before stepping back so that Jazz can take his place and call for volunteers to step forward. Similarly, while Megatron generally gives orders directly and leads from the front, when he's unable to personally lead a counterattack or defense (e.g. he's overseeing something else or is simply not present) he delegates to Starscream, who then leads the other Decepticons.
In the season 3 episode "Starscream's Ghost", a group of Decepticons made up of Cyclonus, Scourge and a trio of Scourge's huntsmen the Sweeps are pursuing the Decepticon Triple-Changer Octane for his actions in a previous episode note  Octane had discovered the heavily damaged Trypticon following his defeat by Metroplex earlier in the season, and kept quiet about it in the hopes of using Trypticon to gain power for himself . When they arrive at a facility they know is the Decepticon Crypt, Cyclonus orders Scourge to send in one of his Sweeps. Scourge complies and orders one of his Sweeps to investigate, but each of the three declines out of superstitious fear. Annoyed, Cyclonus bypasses the chain of command by threatening to shoot the last one in, prompting all three Sweeps to scramble to get inside. Cyclonus takes a moment to chide Scourge for not enforcing the chain of command (something Scourge agrees with) before ordering him in too.
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Not Always Right had an example where a rude customer turned out to be a soldier. A second customer, annoyed by his behaviour, demanded to know if the solider knew a particular individual, and when the soldier angrily replied said individual was his superior the second customer retorted that he was his superior, and that as soon as he got back to base he'd make sure to inform his subordinate of his own subordinate's behaviour. The soldier quickly left.
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Dragon Ball Fighter Z has a mild example when Freeza and the Ginyu Force encounter the heroes. When he decides to withdraw, he gives orders to Ginyu, who then orders his subordinate Guldo to paralyze the heroes with his psychic powers, allowing the villains to escape.
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Fallout: New Vegas allows removing the Elder from the Brotherhood of Steel for violating the Chain That Binds, because the Elder skipped ranks when giving orders concerning the security of the bunker.
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In Super Robot Wars 30, Mitsuba Greyvalley is eager to link up with the Ra Callium commanded by Bright, and when they finally meet she offers him command of the unified heroes (as she's technically just an officer cadet while he's a veteran commander). Bright declines and says he'll only join if she remains in command, explaining that he believes she'd do a better job considering the Mildly Military nature of the unit. He also points out that she was directly appointed by Commodore Filke, and so it wouldn't be appropriate for him to just take charge without at least consulting the Commodore first.
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Schlock Mercenary: A few of The Seventy Maxims of Maximally Effective Mercenaries have something to say about this:
2: A sergeant in motion outranks a lieutenant who doesn't know what's going on.
3: An ordnance technician at a dead run outranks everybody.
63: The brass knows how to do it by knowing who can do it.
69: Sometimes rank is a function of firepower.
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xkcd: Parodied in "Chain of Command" which points out that no one has more authority than the person who actually gives someone the trigger for a weapon...in this case, the US nuclear arsenal.
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Super Robot Wars sometimes plays with the chain of command thanks to the crossover aspect. For example, in Super Robot Wars Alpha, Colonel Bright Noa is the overall head of the combined heroes. However, as a professional courtesy, when faced by the Space Monsters he defers to Captain Tashiro of the Excellion, who has more experience facing them. Conversely, when the cast of Neon Genesis Evangelion join the team, he's informed by NERV commander Gendo Ikari that NERV is given formal authority over any Angel-related conflict and so whenever an Angel appears Major Misato Katsuragi of NERV takes formal operational command.
In Super Robot Wars 30, Mitsuba Greyvalley is eager to link up with the Ra Callium commanded by Bright, and when they finally meet she offers him command of the unified heroes (as she's technically just an officer cadet while he's a veteran commander). Bright declines and says he'll only join if she remains in command, explaining that he believes she'd do a better job considering the Mildly Military nature of the unit. He also points out that she was directly appointed by Commodore Filke, and so it wouldn't be appropriate for him to just take charge without at least consulting the Commodore first.
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Transformers: Super-God Masterforce: Both sides are explicitly described as being independent units separate from the main Autobot and Decepticon forces (who are mentioned as continuing their battles in deep space and so unable to assist on Earth). Metalhawk is initially leader of the Autobot forces on Earth and keeps in touch with Fortress to keep him updated. He later steps down and has Ginrai take over, and instead focuses on his role as Mission Control. Meanwhile, the Decepticons are initially led by Blood, who then reveals he gets his orders from Giga and Mega. As the series goes on, both sides receive aid and reinforcements from the main armies in the form of Brave Maximus (younger brother of Fortress Maximus) and Black Zarak (a rebuilt and upgraded version of Scorponok from the previous series). The death of Black Zarak at the end of the series is described in ancillary material as leaving the Decepticons in disarray until Overlord manages to rally a chunk of their forces.
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Crimson Tide: A big part of the drama comes from the fact that Both Sides Have a Point in regards to the chain of command: Captain Ramsey wants to execute the orders they managed to receive, but Executive Officer Hunter argues that since another set of orders were Lost in Transmission they ought to hold back until they're able to confirm said orders (in case the interrupted orders were meant to rescind the first ones). In addition, Ramsey feels Hunter ought to step back in line and follow his orders, as he's the commanding officer of the submarine. Hunter meanwhile feels that due to the fact they're dealing with nuclear weapons they need to be absolutely sure that they're not wrong, because otherwise they'll inadvertently set off World War III.
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In The Transformers: All Hail Megatron the Decepticons launch what is later known as "The Surge", a massive all-fronts offensive thanks to the traitorous Sunstreaker leaking communication protocols. This is the closest the Decepticons have come to a clear victory in thousands of years, as they launch simultaneous attacks that prevent the Autobots from reinforcing each other and the writer has Optimus Prime take a big chunk of his command staff (Jazz, Prowl, Hound, Ironhide) and then blunder into a trap that takes them out of action for most of the event.
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Avatar: The Last Airbender: As part of his plans to capture the Avatar, Commander Zhao of the Fire Nation Navy approaches Colonel Shinu hoping to make use of his elite Yuyan Archers. Dismissing the hunt as a vanity project, Shinu declines. However, at that moment a messenger hawk arrives informing Zhao of his promotion to Admiral, and so he smugly informs Shinu that "my request is now an order." Shinu complies, and the Archers do indeed manage to capture Aang.
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Band of Brothers: In episode "The Breaking Point", Col. Sink rebukes Major Winters when the latter expresses an urge to run towards his (former) company and try to salvage a battle, telling him he must respect the chain and delegate authority. Winters thus instead appoints a new company commander in Lt. Speirs to relieve the befuddled Lt. Dike.
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Star Trek:
Star Trek: The Original Series:
The series makes clear on several occasions that the chain of command on the Enterprise goes from Kirk, to Spock, to Scotty, though there is debate on who comes next after Scotty (consensus seems to have settled on Sulu). Dr. McCoy, though outside the chain of command, has the authority to circumvent it in his capacity as Chief Medical Officer, and sometimes threatens this on Kirk or Spock. Being outside the chain of command also apparently allows him to openly question and challenge the orders of his superior officers without reprimand; he is the only one who does this, except in extreme circumstances. Both Kirk and even Spock generally allow it, although they do have their limits.
Star Trek: The Next Generation:
"Chain Of Command" has another captain (Captain Jellico) take temporary command of the Enterprise while Captain Picard participates in a secret mission, and when Picard is captured by the Cardassians Jellico continues to command the Enterprise during the crisis. His Control Freak leadership style conflicts badly with the Mildly Military atmosphere encouraged by Picard, to the point that Riker becomes so insubordinate Jellico relieves him of duty. In an example of Both Sides Have a Point, Riker is correct in that Jellico is negatively impacting morale, but Jellico is also absolutely correct that as a professional, Riker should've kept his personal feelings to himself and carried out his duties. It also doesn't help that Jellico is preparing the Enterprise for a potential war, meaning that he doesn't have time or the inclination for the more polite tone Picard tends to use.
"Gambit" has Data assume command of the Enterprise due to both Picard and Riker being out of commission (due to them accidentally getting caught up with the smugglers the Enterprise is investigating). Worf acts as his Executive Officer, but after he openly expresses his displeasure with Data's decisions Data is forced to quietly confront him. While he concedes Worf's point that an Executive Officer ought to offer alternatives to the captain, the issue was that when Data made a decision Worf disagreed with he made that displeasure clear in front of the crew, thus undermining Data's command. Worf accepts Data's argument and apologises.
Star Trek: Discovery: One of the complaints about the series is how there is blatant disrespect for the chain of command, with crewmen often talking back to or snarking at their superior officers. Even taking into account the Mildly Military nature of Starfleet, such unprofessional behaviour was so blatant that it broke Willing Suspension of Disbelief.
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Gargoyles: In addition to the Clan Leader, there is also the position of Second, formerly held by Goliath when Hudson was in charge and then by Demona before her Face–Heel Turn. When they got transplanted to Manhattan the gargoyles became rather lax about that (when they were initially reawakened, there were only 6 of them left), but an incident wherein Goliath got injured caused him to revive the practice, with Brooklyn gaining the title. This became important when Goliath, Elisa, and Bronx disappeared on their world tour, forcing Brooklyn to assume command to prevent their enemies from taking advantage of Goliath's absence.
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Transformers: Prime: The chain of command is Played for Drama when Ultra Magnus joins the cast in Season 3. As a strict military man who was the Autobot military commander during the war on Cybertron, Magnus is a firm believer in the chain of command and maintaining proper protocol. Unfortunately, he has difficulty wrapping his head around the fact that Team Prime are True Companions and function more like a family than a military unit, so his attempts at introducing formal military discipline make things very awkward. Notably, Optimus Prime and Ultra Magnus himself both recognise this, and take steps to try to ease Magnus into the team. At the very least, he's the formal second-in-command of the team (prior to this, Ratchet was informally second in command by virtue of being Optimus Prime's oldest friend and closest confidant).
On the Decepticon side, the Command Roster is Megatron as leader, Starscream as second-in-command, Soundwave as the communications officer and Knock-Out as chief medic (with Breakdown as Mook Lieutenant). When Starscream becomes a Dangerous Deserter late in Season 1, Airachnid takes his place as second-in-command. During the Season One finale, Megatron has gone missing (he formed an Enemy Mine with the Autobots to prevent Unicron from reviving) and in his absence she decides to take the Decepticon warship Nemesis and leave Earth (and Megatron) behind. She orders Soundwave to set course, but when she attempts to pull rank on him and threaten him into obedience he quickly puts her in her place. In an example of how it's one's position within a chain of command (and not necessarily their rank) that provides authority, despite "merely" being the communications officer, Soundwave's actual role is The Dragon.
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Part of the reason Leandros from Warhammer 40,000: Space Marine is so disliked is because despite protesting that many of Captain Titus' actions "are not supported by the Codex Astartes", in the ending it's shown that he's reported his suspicions of Captain Titus being tainted by the Warp to the Inquisition instead of his Chapter's Chaplains and Librarians like he's supposed to. note To explain, the Space Marines really, really, really do not like the Inquisition poking their nose in their business, since there are far too many cases of overzealous Inquisitors declaring Space Marines tainted and having them (and sometimes their entire Chapter) purged. This is a case where going over the head of his direct superior (in this case Captain Titus) would be the correct course of action, but Leandros instead completely ignores the chain of command and reports to an outside organisation instead. Ancillary material suggests that as a result of his actions, he's treated as a pariah by the other Ultramarines, and unlikely to ever get promoted out of his current rank of Battle Brother (the lowest rank).
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Some video games set in the Gundam expanded universe play with the chain of command, one typical example being the protagonists answering directly to someone high up enough the chain that they are able to go wherever they're needed (thus allowing them to participate in some of the famous battles of the original Mobile Suit Gundam without being chained to a particular theatre). An example of this is the Midnight Fenrir unit from Mobile Suit Gundam 0079: Zeonic Front, which answers directly to Kycillia Zabi and often shuffled around various theatres of war as the need arises.
Zeonic Front also expands on M'Quve's failure at Odessa as mentioned in the Anime section above: while abandoning his still-fighting troops was awful, it was understandable that such a high-ranking commander couldn't be allowed to fall into Federation hands. What Midnight Fenrir commander Schmitzer found particularly odious is that when M'Quve fled the battlefield into space, he didn't bother leaving behind a functional chain of command. This led to confusion amongst the remaining defenders who were unable to coordinate the defense and so slaughtered piecemeal by the overwhelming Federation attack.
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In The Transformers (IDW), Prowl expresses frustration with the fact that the Autobots don't seem to take the chain of command seriously and opt to listen to charismatic "heroes" rather than actual superiors. The Wreckers, the Monsterbots and the Dynobots are examples of units that completely ignored chain of command and basically went off doing whatever they wanted. Both the Monsterbots and Dynobots ended up being branded as renegades and deserters, though Grimlock got the other Dynobots pardoned by capturing Scorponok and Shockwave and turning over proof that he'd lied to the others about their mission, so they thought they were following an order from Optimus Prime. To Prowl's disappointment, even Optimus Prime seemed to prefer taking the advice of Hot-Blooded-types like Ironhide or Kup than someone Boring, but Practical like him, despite Prowl's entire job being the strategist. This bites the Autobots in a big way during The Surge, when the Decepticons launched an all-out attack on all Autobot holdings simultaneously. After the Megaseries ended, however, Prowl's characterization began to change and he was shown to have had much more command and authority all along, to the point that he'd been able to run missions that Optimus Prime never found out about.
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Transformers: War for Cybertron: In the first level of the Autobot campaign (which chronologically takes part after the Decepticon campaign), the Autobots defending their capital of Iacon are pushed to the brink by the Decepticons due to their leader Sentinel Prime going missing (in truth he'd been captured by Megatron). They only manage to drive the Decepticons back when Optimus assumes command and rallies them, issuing orders to Jetfire (commanding their air forces), putting Ratchet in charge of holding a forward command post to act as Mission Control, and personally leading the defense on the ground. After becoming Optimus Prime, he actually spends less time on the field due to being more useful actually directing the war effort.
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Star Trek: The Original Series:
The series makes clear on several occasions that the chain of command on the Enterprise goes from Kirk, to Spock, to Scotty, though there is debate on who comes next after Scotty (consensus seems to have settled on Sulu). Dr. McCoy, though outside the chain of command, has the authority to circumvent it in his capacity as Chief Medical Officer, and sometimes threatens this on Kirk or Spock. Being outside the chain of command also apparently allows him to openly question and challenge the orders of his superior officers without reprimand; he is the only one who does this, except in extreme circumstances. Both Kirk and even Spock generally allow it, although they do have their limits.
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Warhammer 40,000
Because of the sheer size of the Imperium of Man, just about any problem that can come up due to a chain of command comes up. Interservice Rivalry, Right Hand Versus Left Hand, Jurisdiction Friction, slow reactions, you name it, it's probably happened. There are several examples of calls for reinforcements received and troops dispatched decades or even centuries after the planet that made the request has either fallen or been outright destroyed.
Among Loyalist Space Marines, whenever Chapters come together there is nearly always some friction as to the chain of command, especially when rivalries get involved. Even when successor Chapters from the same legion meet up, there can be friction. However, this is averted if the original Chapter (e.g. the Salamanders, the Ultramarines, the Imperial Fists) are present, as they automatically take command of their successor Chapters. For example, when the Blood Angels summoned their successor Chapters to help prepare the defense of their homeworld of Baal against the Tyranids, Commander Dante of the Blood Angels took command of all the Chapters that arrived (incidentally, the only Chapter that didn't return for the conflict was the Lamenters, and Dante admitted he wasn't even sure if the Lamenters were even alive due to their reputation as a Cosmic Plaything).
The Alpha Legion is infamous for not having a static chain of command, completely averting Decapitated Army. Each Alpha Legionnaire is trained to be able to assume command in case his superior is killed, and each squad is drilled to already know their mission objectives so even the loss of a commander barely slows them down. This also grants them a huge amount of flexibility, since they're able to respond to changes on the battlefield much faster than other factions. Fitting, considering their emblem depicts a Hydra.
The Emperor's Adeptus Custodes don't really have a chain of command barring their leaders the Captain-General and his advisors the Tribunes. There are Shield-Captains who command units of Custodes, but they're generally chosen from the ranks for specific missions. Generally the Custodes operate as a meritocracy where it's the achievements of the individual Custodes that grant them respect from their fellows, rather than their rank or position. Like the Alpha Legion, this allows them a great amount of flexibility in a fight, as they don't need to report to or request authorisation from higher authorities. Later novels reveal that after the Horus Heresy, the Emperor's surviving loyalist sons drafted an order that restricted the Custodes to Earth and the Imperial Palace. The Custodes publicly adhered to the order... but quietly ignored it and carried on sending secret missions into space because despite being the sons of the Emperor, the Primarchs don't actually have any authority over them.
Among the Traitor Legions, the Iron Warriors are unusual in that they still have an actual chain of command, as opposed to the Asskicking Leads to Leadership Chronic Backstabbing Disorder Klingon Promotion method practiced by most of the other Traitors. The Word Bearers likewise still have a chain of command... in theory. In practice, their Primarch Lorgar doesn't bother much with petty material matters, and their leading council is divided into two opposing camps.
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This Bites!: Luffy is the captain of the Straw Hat Pirates, and all orders from him are final. After Whiskey Peak, he selects Nami and Cross as the Second and Third Mate respectively (with Zoro already being the First Mate) to take charge when he isn't able to or come up with plans that he couldn't, particularly from the tactician Cross.
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Beast Wars: The episode appropriately named Chain Of Command revolves around Optimus Primal going missing, and the Maximals realise they don't actually know who's supposed to be in charge without him. While the former Predacon Dinobot feels that as the best fighter, he should lead, the Maximals Rattrap, Cheetor and Rhinox instead hold a vote... which does nothing when there's a tie between Rattrap and Dinobot with no way to break the deadlock. Luckily, Optimus is able to send a message putting Rattrap in charge.
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Battlestar Galactica (2003): After the Battlestar Pegasus shows up with Admiral Cain on board, Commander Adama notes that she outranks him, and therefore is now in charge of the entire fleet. President Roslin is visibly unsettled to see Adama deferring to Cain and addressing her as "Sir". Cain initially claims she'll respect how Adama runs Galactica, but it doesn't take long for her to start reassinging crewmembers between ships to break up the Galactica crew's unity. She also shows little respect for President Roslin's authority due to her being Secretary of Education the last time Cain heard of her.
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One of the character profiles in The Transformers: Last Stand of the Wreckers is written from the point of view of a Decepticon commander scheduled for execution for assisting the renegade Overlord. He points out that technically Overlord was never actually stripped of his rank and so was still a superior officer, meaning he was simply following the chain of command.
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The chain of command is why in most side stories set during the One Year War period (e.g. Mobile Suit Gundam 0080: War in the Pocket, Mobile Suit Gundam: The 08th MS Team, Mobile Suit Gundam Side Story 0079: Rise From The Ashes), Gihren Zabi is considered the Greater-Scope Villain: since he's Zeon supreme commander he's not involved in the much smaller scale operations of those series other than issuing the strategic objectives (e.g. in 08th MS Team he's the one who authorised the development of the Apsalas Project).
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Spaceballs: In the first scene Colonel Sanders is informed by his subordinate that their target planet is in view, and that the subordinate already informed Dark Helmet. However, Dark Helmet is furious when he learns that the subordinate directly reported the news to President Skroob as well, in his words: "You went over my helmet?" He quickly reminds the crewman of his place.
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One of the plot points in Mobile Suit Gundam is the White Base being designated the 13th Autonomous Corps, giving Bright Noa the freedom to move between theatres of war rather than being tied down to a particular army or fleet. Once they enter a particular theatre, however, they place themselves under the command of the overall commander Example During Operation Odessa, the White Base reported directly to General Revil after uncovering that the general originally slated to command was a Mole in Charge, while during the Battle of Solomon the White Base joined the command of Admiral Tianem . The Final Battle at A Baoa Qu becomes a chaotic mess when General Revil is killed by the Colony Laser along with 20% of the Federation fleet during the approach, meaning that during the battle itself individual fleet commanders are directing their forces as best they can without a higher authority coordinating their efforts.
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Revenge of the Sith has one of the best examples of bypassing the chain of command: Chancellor Palpatine (in his role as head of state) directly contacts the Clone Troopers to initiate Order 66. This is natural, since passing orders down the chain normally would involve going through the Jedi who are serving as generals. In addition, despite having fought under Jedi for years by that point, all the Clones unhesitatingly open fire on their Jedi generals, as they've been trained to be perfect soldiers who follow their orders. note  Post-Disney purchase, a Retcon reveals that the Clone Troopers were Brainwashed and Crazy thanks to a bio chip implanted in their heads.
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Transformers Victory: Star Saber is the supreme commander of the Pan-Galactic Defense Force as well as the Autobots, with Blacker and God Ginrai serving under him as commanders of the Sector 1 and Sector 2 defense forces respectively. In the first episode, it's the presence of Decepticon Emperor of Destruction Deathsaurus nearby Earth that prompts Star Saber to go to Sector 1 and assume command in person. Halfway through the series God Ginrai was mortally wounded and rebuilt as the more unstable Victory Leo, prompting Star Saber to appoint Greatshot as commander of Sector 2. Unusually, it's implied that despite being the Emperor of Destruction, Deathsaurus doesn't actually have absolute control of the entire Decepticon faction, since Overlord is depicted as commanding his own forces having a separate war with his old enemy God Ginrai's Sector 2 forces.
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Babylon 5. The chain of command plays a role in the resolution of "Point Of No Return", when Sheridan realises that the order for Nightwatch to assume control of security operations and to implement martial law comes from the Political Office, a civilian organisation with no authority over the military. This allows him to arrest the members of Nightwatch for technically participating in a mutiny, as they were following an illegal order.
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Transformers
The Transformers: Whenever the Autobots are shown preparing to mobilise (especially in the "More Than Meets The Eye" miniseries that began the series), Optimus Prime issues the orders to his lieutenant Jazz, who then assembles the Autobots and informs Optimus when they're ready. In the final part of the miniseries the Autobots prepare to launch a Death or Glory Attack on the Decepticon encampment. Optimus Prime gives a Rousing Speech to the Autobots (and their human allies Spike and Sparkplug) before stepping back so that Jazz can take his place and call for volunteers to step forward. Similarly, while Megatron generally gives orders directly and leads from the front, when he's unable to personally lead a counterattack or defense (e.g. he's overseeing something else or is simply not present) he delegates to Starscream, who then leads the other Decepticons.
In the season 3 episode "Starscream's Ghost", a group of Decepticons made up of Cyclonus, Scourge and a trio of Scourge's huntsmen the Sweeps are pursuing the Decepticon Triple-Changer Octane for his actions in a previous episode note  Octane had discovered the heavily damaged Trypticon following his defeat by Metroplex earlier in the season, and kept quiet about it in the hopes of using Trypticon to gain power for himself . When they arrive at a facility they know is the Decepticon Crypt, Cyclonus orders Scourge to send in one of his Sweeps. Scourge complies and orders one of his Sweeps to investigate, but each of the three declines out of superstitious fear. Annoyed, Cyclonus bypasses the chain of command by threatening to shoot the last one in, prompting all three Sweeps to scramble to get inside. Cyclonus takes a moment to chide Scourge for not enforcing the chain of command (something Scourge agrees with) before ordering him in too.
Beast Wars: The episode appropriately named Chain Of Command revolves around Optimus Primal going missing, and the Maximals realise they don't actually know who's supposed to be in charge without him. While the former Predacon Dinobot feels that as the best fighter, he should lead, the Maximals Rattrap, Cheetor and Rhinox instead hold a vote... which does nothing when there's a tie between Rattrap and Dinobot with no way to break the deadlock. Luckily, Optimus is able to send a message putting Rattrap in charge.
Transformers: Prime: The chain of command is Played for Drama when Ultra Magnus joins the cast in Season 3. As a strict military man who was the Autobot military commander during the war on Cybertron, Magnus is a firm believer in the chain of command and maintaining proper protocol. Unfortunately, he has difficulty wrapping his head around the fact that Team Prime are True Companions and function more like a family than a military unit, so his attempts at introducing formal military discipline make things very awkward. Notably, Optimus Prime and Ultra Magnus himself both recognise this, and take steps to try to ease Magnus into the team. At the very least, he's the formal second-in-command of the team (prior to this, Ratchet was informally second in command by virtue of being Optimus Prime's oldest friend and closest confidant).
On the Decepticon side, the Command Roster is Megatron as leader, Starscream as second-in-command, Soundwave as the communications officer and Knock-Out as chief medic (with Breakdown as Mook Lieutenant). When Starscream becomes a Dangerous Deserter late in Season 1, Airachnid takes his place as second-in-command. During the Season One finale, Megatron has gone missing (he formed an Enemy Mine with the Autobots to prevent Unicron from reviving) and in his absence she decides to take the Decepticon warship Nemesis and leave Earth (and Megatron) behind. She orders Soundwave to set course, but when she attempts to pull rank on him and threaten him into obedience he quickly puts her in her place. In an example of how it's one's position within a chain of command (and not necessarily their rank) that provides authority, despite "merely" being the communications officer, Soundwave's actual role is The Dragon.
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Despite their codenames, both Steve Rogers and Carol Danvers as Captain Marvel actually hold much higher ranks than Captain, allowing them to order regular US troops around when necessary. On one occasion, Carol tried to pull rank on Cap by stating that she had the rank of Colonel in the air force and demanding that Cap obey her, but Cap retorted that he's ranked Brigader General (presumably thanks to seniority).
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Star Trek: The Next Generation:
"Chain Of Command" has another captain (Captain Jellico) take temporary command of the Enterprise while Captain Picard participates in a secret mission, and when Picard is captured by the Cardassians Jellico continues to command the Enterprise during the crisis. His Control Freak leadership style conflicts badly with the Mildly Military atmosphere encouraged by Picard, to the point that Riker becomes so insubordinate Jellico relieves him of duty. In an example of Both Sides Have a Point, Riker is correct in that Jellico is negatively impacting morale, but Jellico is also absolutely correct that as a professional, Riker should've kept his personal feelings to himself and carried out his duties. It also doesn't help that Jellico is preparing the Enterprise for a potential war, meaning that he doesn't have time or the inclination for the more polite tone Picard tends to use.
"Gambit" has Data assume command of the Enterprise due to both Picard and Riker being out of commission (due to them accidentally getting caught up with the smugglers the Enterprise is investigating). Worf acts as his Executive Officer, but after he openly expresses his displeasure with Data's decisions Data is forced to quietly confront him. While he concedes Worf's point that an Executive Officer ought to offer alternatives to the captain, the issue was that when Data made a decision Worf disagreed with he made that displeasure clear in front of the crew, thus undermining Data's command. Worf accepts Data's argument and apologises.
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Captain Atom sometimes has to deal with the fact that as a serving member of the US military, he has to take orders from superior officers that might conflict with his ideals as a superhero.
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