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Over-the-Top Secret

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You know the trope. In order to emphasize just how ridiculously important something is, it is classified as "Above Top Secret." Maybe it has a special name, maybe it doesn't, but the point is that high-ranking people who thought they were privy to every secret are...not. The head of an intelligence agency may come across a locked computer file requiring "Level 11" security clearance or some other fictional requirement.
This trope is the result of a common misconception about Security Clearances. In Real Life, just because you have a "Top Secret" security clearance doesn't mean you can read through the files of Area 51 or peruse Black Site files at your leisure. You still need to demonstrate a "Need to Know", a justifiable reason why you should have that information.
For example, a person working on destroyers would need to know information about destroyers, and might need to know details about cruisers if trying to work out doctrine in which the two classes of ship work together, but said person would have no reason to ask about tanks while on his current assignment.
Unfortunately, in fiction, "Need to Know" is generally just a mechanism used to postpone telling people things they DO need to know until some point after the moment when knowing the information would have helped. When someone talks about having "Code Word Clearance", they mean that the code-word of a particular project or operation is listed in their security file, which means that they can access any information filed under that code-word.
This is also why anyone talking about information being classified "Above Top-Secret" is ridiculous, since you can use the same compartmentalizing system to isolate especially sensitive information. And those compartmentalized systems often require an additional Sensitive Compartmented Information and/or Special Access Program clearance in addition to a regular TS. Which can be made even more complicated if it includes information regulated by the Department of Energy.
See also Classified Information, and Serial Escalation. If an entire organization is classified as such, you're likely looking at an instance of No Such Agency.
Not to be confused with Above Top Secret, which is a website about conspiracy theories.
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In season 2 of Agents of S.H.I.E.L.D., Coulson mentions that they got rid of the levels when they rebuilt S.H.I.E.L.D. after the events of Winter Soldier, implying a more traditional "need to know" structure.
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In Star Trek: Discovery, there's the Battle near Xaeha, in which the Discovery, the Enterprise, the Klingons and others teamed up to battle the mad AI Control. Officially, Discovery was lost with all hands, but only a select few know they actually jumped to the future and that truth is also under lock and key to prevent Control from returning.
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In Paranoia, the highest security clearance is Ultraviolet. Everyone knows this. The Iceman Returneth features clones of a couple of The Computer's original programmers from the Old Reckoning, assigned Gamma Clearance and entrusted with maintaining its core systems. Later editions mention rumors that Gamma Clearance or something like it exists, which even Ultraviolets are warned not to discuss without clearly stating that it doesn't— and even if they believe otherwise, probably the best they can do is manipulate their rivals into prying into the subject and getting busted for it.
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Seven Days
The project itself is so classified that the President knows nothing about it. After a couple of encounters with Parker, he does know he is part of something and is determined to find out. His clearance is insufficient.
There was an episode where Parker had a run-in with some unit, and stated he had a very high clearance level. A soldier from the unit stated that he has a level high enough to shoot Parker on the spot.
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Distance Learning for Fun and Profit...: When PRT Director Costa-Brown (secretly Alexandria) demands to know the identity of the Tinker behind Gravtec, arguing she has top secret clearance, she is told that (a) the responsible individual is not a Tinker, so it falls outside her remit, and (b) her clearance is irrelevant.
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The Headhunt establishes the Federation Starfleet as using a two-layer clearance system inspired by real life systems. Before briefing her security chief on a break-in at Facility 4028 Eleya double-checks his security clearances. Dul'krah is cleared to see any data classified up to sigma-9, and can view data classified up to chi-4 if he's cleared for the code word. The relevant file is classified lambda-5 under the code word ICARIAN BRIGHT GEPPETTO.
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The Weaver Option: Before Taylor takes over the Nyx Sector, there is an absurdly large number of secret clearances due to previous administrations' corruption. Part of her government's work is to streamline this, resulting in a color-coded clearance system. Taylor herself doesn't have access to the top-level clearance, which is restricted to Inquisitors.
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In Alpha Protocol, the titular program is stated to 'not exist.' "And the agencies that suspect we might exist? They don't exist either." It's so top secret that no one even knows where the base is; even top-level agents are drugged unconscious and shipped halfway around the world before being woken up.
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The trope is discussed directly a few times in Stargate SG-1:
In "Touchstone" Col. Maybourne tells SG-1 that they're not cleared for some information; they point out they have the highest possible security clearance, and Maybourne says that that's only true within the military, and Area 51 is a civilian operation.
The team themselves often have to tell Muggles they run into that what they're doing is classified. In "Seth" they claim jurisdiction over an investigation into a cult (the cult leader was an undercover Goa'uld). The officer in charge protests and says that he has "top-level clearance", to which O'Neill replies "Not top enough." He is finally convinced to shut up and do what O'Neill says when none other than the President of the United States calls him and confirms the team's authority.
And then of course there's the page quote, where the Chairman of the Joint Chiefs is briefing the newly elected President Hayes on the Stargate program.
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The characters of Spooks often talk about various classifications of files in regards of how tightly their contents are meant to be protected. The series 4 episode 'Diana' goes so far as to mention a "No Eyes" file: one that was never meant to be taken out of the room it was stored in.
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SCP Foundation: In one 001 proposal, the newly appointed O5 council tries to figure out why O5-13 is the only one around from the old council. When they ask the Ethics Committee, they get the answer that it is "Above [their] clearance".note Some stories imply that the Committee has equal, or even higher security clearance than the O5s.
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Tora! Tora! Tora!: It is mentioned early on that the President and his staff are not cleared to directly handle or view any of the signal decripts of Japanese message traffic due to a past incident where one such decrypted message was found in an office wastebin rather than properly disposed of. Thus, the absurd situation where the Commander in Chief of the United States Armed Forces effectively lacks the clearance for some of the information the military is handling.
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Iron Helix: The very existence of the Iron Helix weapon was so secret that the crew of the ship that was transporting it didn't even know they were transporting it.
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The Stargate Program in the Stargate-verse.
In a variant, it's only above top secret for the United States— China insists that they are not going to make any effort to help America maintain The Masquerade, and Russia and other countries are only placated by giving them stakes in the Atlantis mission and similar expeditions.
The trope is discussed directly a few times in Stargate SG-1:
In "Touchstone" Col. Maybourne tells SG-1 that they're not cleared for some information; they point out they have the highest possible security clearance, and Maybourne says that that's only true within the military, and Area 51 is a civilian operation.
The team themselves often have to tell Muggles they run into that what they're doing is classified. In "Seth" they claim jurisdiction over an investigation into a cult (the cult leader was an undercover Goa'uld). The officer in charge protests and says that he has "top-level clearance", to which O'Neill replies "Not top enough." He is finally convinced to shut up and do what O'Neill says when none other than the President of the United States calls him and confirms the team's authority.
And then of course there's the page quote, where the Chairman of the Joint Chiefs is briefing the newly elected President Hayes on the Stargate program.
Stargate Atlantis occasionally had the cast complaining that they couldn't tell anyone back home where they were because it was classified. This came to a head at the end of the first season, where everyone records a farewell message to their loved ones, just in case they don't survive. Zalenka's message is an enthusiastic, detailed description of Atlantis rising up from the ocean floor (in unsubtitled Czech). Lt Ford then asks if he said anything that would require security clearance. Zalenka gets an Oh, Crap! expression.
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Frequently invoked in Hullo Russia, Goodbye England, where the pilots of the Vulcan nuclear bomber force are under continuing and unremitting security surveillance. One, Flight Lieutenant Silk, is under suspicion because his wife is a member of Parliament associated with the Campaign for Nuclear Disarmament.
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The X-Files is filled with these, some of which being so secret that it seems no one really seems to know the secret information, only knowing bits and pieces of it.
This is shown in "Dreamland" when Mulder accidentally infiltrates The Men in Black and finds they've got no idea if aliens exist either. The Imported Alien Phlebotinum is developed elsewhere and their job is just to protect it.
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Marvel Cinematic Universe:
One-Shot The Consultant sees SHIELD Agent Jasper Sitwell realizes this, then lets it slide, since he's talking to a right-hand man of the director, they're both highly ranked, and considering the nature of secrets kept, there are some things better off not known.
Note that Agents of S.H.I.E.L.D. states that Coulson is level 8note  He'd been promoted since the events of The Avengers. Keen-eyed viewers would note that his ID badge in the movie reads "Level 7". At the end of the first season, it gets bumped to 10, as Fury chooses him to be the new director, and there are still some things he isn't cleared to know.
In Captain America: The Winter Soldier, Cap is also Level 8, and Nick Fury's level is 10. The intrigue starts when Fury discovers information that even he cannot access, supposedly sealed on his own authority. By the end of the film, however, all of S.H.I.E.L.D.'s secrets are public knowledge.
In season 2 of Agents of S.H.I.E.L.D., Coulson mentions that they got rid of the levels when they rebuilt S.H.I.E.L.D. after the events of Winter Soldier, implying a more traditional "need to know" structure.
As of season 4, the new Director replaces the levels with a color-based clearance scheme. The intent was to keep agents from feeling like they were being ranked in importance, but it ended up just confusing everyonenote It appeared to be an indication of category clearances, so green = blue + yellow indicates that someone with green clearance has access to data classified in categories blue and yellow, but not red. The Byzantine clearance structure is mocked several times, with characters noting that they have no idea what Daisy's Blue clearance actually means, and in a later episode Gen. Talbot half-jokingly offers Simmons "Day-Glo Pink" clearance if it will get results.
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The Goodies are poking around a secret military research base and find files marked TOP SECRET (please take one), RATHER MORE SECRET, SPECIALLY SECRET, and EVER SO SECRET.
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In GI Joe The Rise Of Cobra, the title organization is described as above top secret. Of course, sometimes it seems like everyone on the planet knows about them, so it's one of those examples. Then in the sequel, the COBRA President of the United States publicly announces GIJOE's destruction, no doubt leaving the entire world to wonder what he was talking about.
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Aporia: After Chrysalis's disastrous attack at the Canterlot Wedding, Shining Armor receives a report from the Equestrian Office of Special Investigations which is labeled "Over The Top Secret, Burn Before Reading". Needless to say, he finds the whole thing ridiculous — as does Spike, who ends up following said instructions a moment later.
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Anyone who even mentions General Warren Monger's secret monster storehouse in Monsters vs. Aliens receives a dart to the neck and passes out instantly.
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The terrorist organization Cerberus was like this in Mass Effect: an Alliance Navy admiral had to go to the Shadow Broker in order to find anything at all about them. Then came Mass Effect 2 and that was thrown completely out the window in favor of them being a group that everyone knows about who slaps their logo on everything remotely related to them.
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Scandal sometimes deals with government secrets that are deemed too sensitive to be revealed to the President's Chief of Staff or even the President himself. In particular the work Huck did for the government was so horrifyingly illegal that his record is kept secret from the White House even after Huck becomes the main suspect in an attempt on the President's life.
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Independence Day: The Secretary of Defense has kept the existence of a recovered spaceship and alien corpses at Area 51 a secret even from the President, in order to maintain Plausible Deniability, so the President doesn't learn about the secret laboratory beneath Area 51 until Julius Levinson confronts them and the truth comes out. The Chairman of the Joint Chiefs of Staff points out that a good time to share this secret would have been some time after the aliens themselves arrived in force over Earth and before the military launched a fruitless attack against them without knowing anything about their capabilities.
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Joked about in The Forgotten, where cops talk about the Feds muscling in on their investigation, stating that he would say “God only knows� what they're doing, but he's no sure that He is in the loop.
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In The Laundry Files, the Laundry is classified under a portion of the British Official Secrets Act that is itself classified: if you know about it, you're required to sign it in blood (to create a magical oath binding your tongue) to say that you won't reveal it. The Laundry itself uses a code word system to determine clearance for various projects and documents: main protagonist Bob Howard tells a security reviewer at one point that he and his wife Mo, also a Laundry officer, are careful to compare code words before discussing work, and Bob once fires off a very irate phone call to his superior to get himself cleared for whatever mission Mo just came home from that left her on the verge of a nervous breakdown if she can't talk to someone about it.
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Blake's 7
In "Animals", Double-X information can only be passed verbally, with no stored records. Servalan has to track down a member of the project team and deliver some unsubtle threats before finding out what she wants to know, and she's a commissioner in the Secret Police at the time.
The crew of the Liberator encounter the planet Horizon at the edge of the galaxy when they nearly run into the forceshield protecting it. There's no information on the planet whatsoever in their databanks, so they later get a pursuing Federation flotilla to destroy itself by colliding with the same forceshield, betting their lives on the likelihood that the Federation mooks won't be any better informed.
Finding the location of Star One (a base containing the Master Computer which controls the Federation) is the Story Arc for Season Two. It's so secret that anyone who could possibly know its location has either been killed or brainwashed into forgetting it. This backfires badly because when things start going wrong with Star One, even the people running the Federation don't know where it is!
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Deus Ex first introduces its own fictional security clearance hierarchy used within UNATCO, with nine levels of security named after the Hierarchy of Angels, and then applies this trope by later revealing there is "God-level" clearance even above that.
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In Men in Black 3, J is told that the exact details of what happened between his partner K and Boris the Animal is above his pay grade. He's a senior agent only a step or two below the chief, so he's quite surprised. Shortly thereafter, he finds out about time travel— which is also above his pay grade.
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In Captain America: The Winter Soldier, Cap is also Level 8, and Nick Fury's level is 10. The intrigue starts when Fury discovers information that even he cannot access, supposedly sealed on his own authority. By the end of the film, however, all of S.H.I.E.L.D.'s secrets are public knowledge.
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Phantom Doctrine: "Above Top Secret" is the title of the first chapter in the KGB campaign, alluding to the counter-intelligence nature of Agent Kodiak's cell on trying to weed out agents within the Soviet bureaucracy. The local militsiya are not on your side, for instance.
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There's an episode of The Avengers (1960s) where it's mentioned that British Intelligence has at least two secrecy classifications: "Top Hush" for regular top secret material, and for anything exceptionally sensitive, "Button Lip".
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New Avengers: Despite being Director of SHIELD, and therefore supposedly privy to all SHIELD info, Maria Hill is exasperated to find out there's still things the tech people keep from her, even during a serious situation.
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Stargate Atlantis occasionally had the cast complaining that they couldn't tell anyone back home where they were because it was classified. This came to a head at the end of the first season, where everyone records a farewell message to their loved ones, just in case they don't survive. Zalenka's message is an enthusiastic, detailed description of Atlantis rising up from the ocean floor (in unsubtitled Czech). Lt Ford then asks if he said anything that would require security clearance. Zalenka gets an Oh, Crap! expression.
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In Transformers (2007), a high-ranking Sector 7 officer shows the Secretary of Defense some video of a Decepticon taken by a Mars probe that was reported having crashed, saying that it was "classified above top secret" by President Herbert Hoover (in the 1930's).
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The following is a list of statements referring to the current page from other pages.

 Over-the-Top Secret
processingCategory2
Espionage Tropes
 Over-the-Top Secret
processingCategory2
The Secret Index
 A Leaf of the Tree (Fanfic) / int_d49291cd
type
Over-the-Top Secret
 Distance Learning for Fun and Profit... (Fanfic) / int_d49291cd
type
Over-the-Top Secret
 Independence Day / int_d49291cd
type
Over-the-Top Secret
 Transformers / int_d49291cd
type
Over-the-Top Secret
 Transformers (2007) / int_d49291cd
type
Over-the-Top Secret
 Valerian and the City of a Thousand Planets / int_d49291cd
type
Over-the-Top Secret
 Mageworlds / int_d49291cd
type
Over-the-Top Secret
 Rogue Warrior / int_d49291cd
type
Over-the-Top Secret
 Starship Troopers / int_d49291cd
type
Over-the-Top Secret
 Killjoys / int_d49291cd
type
Over-the-Top Secret
 The Avengers (1960s) / int_d49291cd
type
Over-the-Top Secret
 Deus Ex (Video Game) / int_d49291cd
type
Over-the-Top Secret
 Iron Helix (Video Game) / int_d49291cd
type
Over-the-Top Secret
 Phantom Doctrine (Video Game) / int_d49291cd
type
Over-the-Top Secret
 [PROTOTYPE] / Videogame / int_d49291cd
type
Over-the-Top Secret
 My Little Pony: Equestria Girls – Forgotten Friendship / int_d49291cd
type
Over-the-Top Secret