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Shielded Core Boss

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A type of Video Game boss whose weak point is protected from your attacks by some kind of regenerative shielding or armor that you must destroy before he'll take any actual damage.
We use the term "shielding" loosely here: In most cases it really is literal shielding or armor plating, but the concept can extend to almost anything the boss uses to block, deflect, or otherwise nullify your attacks.
Unlike the Tactical Suicide Boss, you cannot simply dodge and evade the boss's attack patterns until he leaves you an opportunity to strike. Nor can you depend on something within the room to give you an opening either. Violence is the Only Option when facing a Shielded Core Boss — you must actively attack and destroy this shielding to expose his weak point, then attack again to damage his Life Meter before he can put the shielding back up. Expect to have to take out his shielding multiple times throughout the battle before he is finally defeated.
Some of these bosses can be very difficult, depending on how much damage their shielding can sustain before it is disabled, and how quickly the boss regenerates it. In some extreme cases, damaged (but not destroyed) shielding may even regenerate on its own, requiring the player to not only inflict damage to disable it, but to inflict damage quickly and continuously. On the other hand, some are simply tedious if destroying his shield takes a long time and he doesn't otherwise pose much of a threat; in many such cases a player may opt to take some damage if it means getting some extra hits on the core while it's exposed. The core, once exposed, may also surprise players by lashing out with the boss's most powerful attack.
Distantly related to the Puzzle Boss, since the boss cannot be damaged directly as long as his shielding is in effect; but where a Puzzle Boss will rely on some other, indirect means to take him out, here you must attack the boss just the same.
If the armor does not regenerate throughout the battle, the boss merely has Destructible Armor (and will very likely Turn Red once his armor is destroyed), and a savvy player can use it to calculate their progress towards defeating the boss.
See also Flunky Boss, where the boss is protected by independent Mooks, who may need to be destroyed before you can engage the boss directly; Cores-and-Turrets Boss, in which the boss's presence is reduced to its (no pun intended) core elements — something that attacks you, and something for you to attack — and Broken Armor Boss Battle, where physical armor needs to be shucked off of a boss before any damage can be dealt.
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From the Metroid Prime Trilogy series:
The Emperor Ing in Metroid Prime 2: Echoes provides two examples in one long battle: In its initial form, Samus must destroy its tentacles to expose its weak point for damage; in its final form, hitting its weak point with enough firepower prompts the boss to shield it with either Light or Dark energy, at which point the player can actually damage the boss with the opposite energy weapon.
The gigantic war golem Mogenar in Metroid Prime 3: Corruption has four Phazon cores (in various locations) shielded by red energy orbs; the player must blast through the shielding and then deliver a strike at the core with their Hyper Beam. Mogenar can regenerate the energy orbs using fixtures located along the edge of its Boss Room, and regenerates all of them whenever any core is destroyed. It is considered one of the game's most difficult battles.
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The Gorgon, the boss of Area 6 in Star Fox 64, requires you to shoot three energy balls surrounding its energy core before it will take damage. After a short window of opportunity, it generates three large metal tendrils and closes its shell entirely; you must shoot and destroy the tendrils to open the shell, then repeat the process all over again. You need to destroy those three energy balls three times in a row before you can properly shoot the core and destroy the Gorgon.
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Devil May Cry: In the first phase of his boss fight, Mundus periodically summons four magical orbs to create a protective barrier against Dante's attacks.
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Devil May Cry 2: Jokatgulm subverts this. You can bypass hacking away at her tentacles and go straight for her head, but it's a lot easier without her tentacles in the way.
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Devil May Cry 4: Sanctus has a regenerating force field you must destroy to damage him and constantly floats away when you try to close the distance. Overlaps with Tactical Suicide Boss, because the probes that spawn and orbit around him can be grabbed and used to pull yourself towards him - although sometimes he tries to rectify this by making them explode when you're near them.
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Devil May Cry 5: Urizen puts up a shield that Nero or Dante must destroy before he can be damaged. After some time, he will regenerate the shield and while it goes down easier, his attacks became more aggressive and hit much harder.
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In Etrian Odyssey 2 Untold: The Fafnir Knight, the Yggdrasil Core will start the fight with a barrier that protects it against any and all damage and its tentacles must be destroyed to take the barrier down and be able damage it. It'll regenerate the tentacles afer a few turns, bringing the barrier up again with more of them.
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 Etrian Odyssey II: Heroes of Lagaard (Video Game)
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ULTRAKILL: After enough time has elapsed, the central computer brain of the Earthmover will pull Idols out of the floor, making itself unable to take damage until they are destroyed. It can do this multiple times throughout the fight, although it's entirely possible to kill it fast enough that it never gets the opportunity to do so at all.
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The second boss of Frantic Frigates is a submarine protected by a two-layer Orbiting Particle Shield. Instead of taking down the particles, you have to wait for them to suddenly spread out, letting you go inside and beat on the boss. With sufficient upgrades to damage and firing speed, it's possible to take out the boss even before the shield comes back.
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Kingdom Hearts II:
The MCP. While also being harassed by Sark, Sora has to hack through a barrier, presumably a firewall of some sort, and use a special Action Command with Tron to fire a beam at the MCP's core and delete it. The Updated Re-release also has an Optional Boss fight against Vexen, whose shield needs to be destroyed before he can be damaged directly. Half the fun is just getting close enough to do this while avoiding his attacks and keeping him from scanning you, especially since he reforms the shield if you leave him alone for more than a couple seconds.
The Updated Re-release includes an Optional Boss fight against Vexen, whose shield needs to be destroyed before his actual health can be damaged. He'll also respawn his shield in he isn't attacked right after it breaks. Naturally, this also applies to his data battle.
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In Sonic 3 & Knuckles, Robotnik pilots a large stone golem as the boss of Sandopolis Zone Act 2; although it only takes one hit to dislodge the armor and expose Robotnik, the armor quickly snaps back into place, resulting in a limited window to strike.
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From the final chapter in Odin Sphere, the "King of the Underworld" is a gigantic undead Cerberus. Unlike the still-living cerberus you defeated before him, after destroying his three heads you must attack his exposed heart before he regenerates the heads and the process repeats.
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Star Fox: Assault has this in Mission 5 with Pigma, who has become a massive Aparoid creature fused with a space station. The first stage of the fight involves destroying the station's six crane arms before the center opens up, upon which you now have to shoot the massive Aparoidedized face of Pigma.
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Epic Mickey:
All Beetleworx enemies (yes, all of them, even though only one is an actual boss) have a layer of Paint armor that you must dissolve with Thinner before you can deliver a damaging attack. They regenerate their armor after taking each hit.
When Petetronic Turns Red he delivers a Shout-Out to TRON by surrounding himself with rotating energy shields as you deflect his homing energy discs back at him.
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Star Fox:
The Reactor Boss in Star Fox requires you to deactivate its shields before you can damage it. The second version can regenerate them.
The Gorgon, the boss of Area 6 in Star Fox 64, requires you to shoot three energy balls surrounding its energy core before it will take damage. After a short window of opportunity, it generates three large metal tendrils and closes its shell entirely; you must shoot and destroy the tendrils to open the shell, then repeat the process all over again. You need to destroy those three energy balls three times in a row before you can properly shoot the core and destroy the Gorgon.
Star Fox: Assault has this in Mission 5 with Pigma, who has become a massive Aparoid creature fused with a space station. The first stage of the fight involves destroying the station's six crane arms before the center opens up, upon which you now have to shoot the massive Aparoidedized face of Pigma.
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Like the Devil series, Alpha's core from Battle Network 3 is open to attack once you tear open its gelatinous shell with rapid-fire attacks.
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 Mega Man Battle Network 3: White and Blue (Video Game)
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Kero Blaster: In her first phase, possessed Nanao only takes damage when hit directly, which requires shooting off all of the Negativus Legatia blobs covering her body. They reform after she pushes herself back to the opposite side of the screen.
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In Mighty No. 9, Dynatron will create an electric barrier around herself once her HP is reduced to half. This consists of six nodes, and when one is destroyed, the remaining nodes rearrange to form the next regular polygon down. The barrier is destroyed once less than three nodes remain and allows Beck to damage her. She can regenerate these nodes if Beck takes too long to defeat her, though.
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The Elder Scrolls V: Skyrim: Alduin can only take damage after you use Dragonrend to bring him down to the ground where you can attack him.
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In Persona 3, the Hanged Man boss has its three statues. Sometimes the only hit you get on it is the All Out Attack after it falls as it regenerates them immediately after their destruction.
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In Persona 4, the boss of the "Void Quest" dungeon resembles a newborn child, who starts the battle by surrounding itself in a shell resembling a pixelated, 8-bit RPG character sprite. You must destroy the shell to expose the boss itself, although the boss is by no means defenseless while regenerating its shell.
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In Warframe, most bosses have a phase where they're invincible, forcing Tenno to plan around bringing down their source of invincibility before going for the kill. Standout examples include the Eidolons, whose shields are impervious to all forms of damage except for the void energy fired by an amp-wielding Operator., and the Orb Mother bosses, who are immune to attack until their shielding is brought down in the case of the Profit-Taker Orb or their armor is overheated in the case of the Exploiter Orb.
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Devil May Cry 3: Dante's Awakening:
Cerberus is covered in ice armor over his body that needs to broken through to attack his body parts, which he'll restore after at least one ice covering is fully destroyed with some time.
Leviathan's Heart is encased in a hard shell that opens up for a short time when one of two adjacent organs is destroyed. The other organs recover quickly and you are also constantly swarmed by mooks that make it difficult for you to directly attack the heart.
Nevan has an electrical shield that drops when all of the bats surrounding her are destroyed. And then you must instantly attack her at least once or else she'll immediately regenerate the shield to full.
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Resident Evil 4 has this with the Queen Plaga/Salazar/Verdugo chimera; you have to shoot Verdugo's eye so the creature opens up to reveal Salazar, who is its weak point.
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In Shantae: Half-Genie Hero, Ammo Baron spends most of his time surrounding himself with a formation of flying Mooks. You can temporarily knock them out to get a clear shot at the Baron, but reinforcements will periodically fly in.
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The Legend of Zelda:
The Legend of Zelda: A Patra swarm's large central flying eyeball is surrounded by a ring of smaller ones. All of the small eyes need to be defeated before the large one can be taken out.
The Legend of Zelda: Ocarina of Time: Starting with this game, most boss battles typically consist of using a newly-acquired weapon/tool from the latest dungeon to "stun" the boss and expose its weak point to ordinary sword strikes before the boss recovers from it; the entire process is generally repeated three times before the boss dies.
The Legend of Zelda: Oracle Games:
In Ages, Pumpkin Head's true form is a small spirit hiding inside the jack-o'-lantern that forms its head. To harm it, Link must first destroy its body and then toss aside the Jack-o'-Lantern to reveal the spirit, then strike at it while it dashes back to the lantern. Pumpkin Head then reforms its body, and the process repeats several more times to defeat it.
In Ages, Eyesoar's central eye is protected by four smaller eyeballs orbiting around it. Link must shoot the Switch Hook into a gap between the eyeballs in order to stun the central eye, which will cause its entourage to scatter and leave it vulnerable to attack until they re-gather.
In Seasons, Manhandla's weak point is a red core within its body. To defeat it, Link must first destroy its maws and then break through its armor with the Magic Boomerang, after which he will only have a short time to attack the core before Manhandla's body regenerates.
The Legend of Zelda: Skyward Sword:
Ghirahim is the quickest example: in his final battle, you destroy the armor surrounding his core with Fatal Blows. Once he summons a large claymore as his weapon, the only way to finish him off is to chip away and shatter his weapon with repeated sword strikes, then deliver a thrust attack to his exposed core. Get thrown off rhythm and Ghirahim will simply repair the blade with a snap of his fingers.
Koloktos covers its weak point by various means, and the battle proceeds primarily by using the whip to strip them away before striking the core. It goes up a notch when he Turns Red, with Koloktos wielding six gigantic swords while shielding its weak point with an iron grate. One strategy is to detach three of its arms with your whip, then pick up one of those giant swords to knock off its remaining arms, legs, and then smash through the grate and strike its core, which itself must be repeated three times to win the battle.
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Mass Effect 2 has a couple of these: the Reaper core in the Derelict Reaper mission and the rogue VI in the Overlord DLC. In both cases, you have to shoot things around the core first to make it vulnerable.
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Each of the big armor bosses in Shadow Warrior requires blasting away the glowing pieces of armor until the crystalline Ki Line is exposed, at which point you have to blast the hell out of it in order to disable it. Since each armor brings the armor back up after a while, you'll have to do this multiple times for each part that has glowing armor in order to destroy the boss.
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Super Mario Bros.:
A late-game boss battle in Super Mario RPG is the gigantic sword known as Exor. His weak point is the skull on the hilt, but the game informs you that it is protected from attacks by his two eyes. You have to attack and disable at least one of the eyes before you can inflict damage on his weak point, and the eyes revive after a few turns. Due to a Good Bad Bug, the removable protection includes the ability to use Geno Whirl on the boss.
In Paper Mario: The Thousand-Year Door, the Yux enemies can generate Mini-Yux from themselves, which produce shields that can block all damage Mario and his partners can do. The regular and "Z" Yuxes create one mini-Yux per turn, meaning Mario or his active partner can destroy the Mini-Yux while the other harms the Yux directly. The X-Yux, however, generates two per turn, requiring multi-target attacks, or else the X-yux will just create another shield as soon as the last one goes down. Grodus, the Mad Scientist who created these enemies, uses a similar system in battle, where he'll summon two Grodus X units per turn. Each Grodus X reduces damage to Grodus until four of them surround him, upon which they will negate all damage done to Grodus until at least one Grodus X unit is destroyed.
Mario & Luigi: Superstar Saga:
In the rematch against Fawful, he starts off hiding in an invention of his that's completely impervious to damage. However, landing enough hits will provoke him into using a powerful attack that overheats the machine, forcing him to leave it temporarily and make himself vulnerable.
When facing the Final Boss, you must destroy its hands and head in order to expose (and strike) its heart; the hands and head quickly regenerate, requiring you to repeat this process throughout the battle.
Mario & Luigi: Partners in Time: Princess Shroob attacks the brothers on a mechanical throne with a Deflector Shield protecting her. You have to destroy the shield (which notably takes a fixed number of hits regardless of damage), disabling the throne and forcing her to fight on foot, before you can damage her directly. The second fight against the elder Princess Shroob extends this pattern one step further: you cannot damage her until you've destroyed her crown, but you can't strike the crown without attacking her feet to knock her down first. In both cases, the princess recovers after a short while, forcing you to start the process over.
Mario & Luigi: Bowser's Inside Story:
The giant Wiggler. It can only be damaged in the head after all its segments have been turned yellow (you do so by attacking the segments), but it will turn back to red in a short while, forcing you to repeat the process.
The final boss follows in the footsteps of the previous games, but has Bowser fight against Dark Bowser until he knocks the Dark Star Core/Fawful out of him, after which he needs to vacuum it up so the bros. can fight it. This in turn requires them to first destroy both of its glasses' lens so they can destroy its three legs (As the boss simply retract them if the Bros. attack while he can see clearly), then they can finally attack the core and deal some lasting damage. Failure to destroy it in a few turns requires you to repeat the entire sequence beginning from Bowser's part, but thankfully, its HP isn't that high.
Mario & Luigi: Dream Team:
The Pillodium takes little damage until its two wings have been destroyed, after which it'll drop to the ground and suffer from an attack/defense debuff until its wings have been completely repaired by its bits. This process can be slowed down by attacking the partially repaired wings.
The final boss, Dreamy Bowser, will shield his head if the Bros. try to attack it while his right arm is still functioning. Though you can aim for his body with certain attacks, his head takes significantly more damage. Annoyingly, unlike the previous boss, any amount of healing will make his arm function again, and he can start healing himself whenever he wants to, which also forces you to eliminate a mob of his minions before he'll come back and fight you again...
A boss in Super Mario Galaxy, Megaleg, is powered by a Grand Star in a glass dome on its head, and the dome is surrounded by a cage. To beat it, you have to lead a Bullet Bill up to smash open the cage... at which point a spinning wall pops up to protect the dome. Sections of the wall can be destroyed with more Bullet Bills, but after a short time they will regenerate, so you need to lead a Bill though the gap before it closes. Or you can do some fancy jumping to get the Bullet Bill to fly OVER the wall.
In Yoshi's Island, Sluggy the Unshaven's heart is an obvious weak point (despite Kamek's Suspiciously Specific Denial), but hitting it requires getting through the surrounding ectoplasm, which regenerates.
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The Legend of Zelda: Skyward Sword:
Ghirahim is the quickest example: in his final battle, you destroy the armor surrounding his core with Fatal Blows. Once he summons a large claymore as his weapon, the only way to finish him off is to chip away and shatter his weapon with repeated sword strikes, then deliver a thrust attack to his exposed core. Get thrown off rhythm and Ghirahim will simply repair the blade with a snap of his fingers.
Koloktos covers its weak point by various means, and the battle proceeds primarily by using the whip to strip them away before striking the core. It goes up a notch when he Turns Red, with Koloktos wielding six gigantic swords while shielding its weak point with an iron grate. One strategy is to detach three of its arms with your whip, then pick up one of those giant swords to knock off its remaining arms, legs, and then smash through the grate and strike its core, which itself must be repeated three times to win the battle.
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A late-game boss battle in Super Mario RPG is the gigantic sword known as Exor. His weak point is the skull on the hilt, but the game informs you that it is protected from attacks by his two eyes. You have to attack and disable at least one of the eyes before you can inflict damage on his weak point, and the eyes revive after a few turns. Due to a Good Bad Bug, the removable protection includes the ability to use Geno Whirl on the boss.
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Densetsu no Stafy 3: Pengod protects himself from attacks with a ring of ice spheres in three different colors. Attacking a sphere will cause it to change color, and when all spheres are the same color, the ring of spheres will vanish, making Pengod vulnerable to attack. Overlaps with Puzzle Boss.
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Persona:
In Persona 3, the Hanged Man boss has its three statues. Sometimes the only hit you get on it is the All Out Attack after it falls as it regenerates them immediately after their destruction.
In Persona 4, the boss of the "Void Quest" dungeon resembles a newborn child, who starts the battle by surrounding itself in a shell resembling a pixelated, 8-bit RPG character sprite. You must destroy the shell to expose the boss itself, although the boss is by no means defenseless while regenerating its shell.
The first phase of the Final Boss of Persona Q: Shadow of the Labyrinth, the spider at the top of the clock tower, protects itself with four of its legs. Each is tied to a specific element, has its own weaknesses, and attacks independently. The problem is, each leg regenerates on its own timer, so to get the maximum amount of time to attack the boss, the party has to carefully kill them all simultaneously, weathering the maximum amount of attacks per turn in the mean time.
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In Yoshi's Island, Sluggy the Unshaven's heart is an obvious weak point (despite Kamek's Suspiciously Specific Denial), but hitting it requires getting through the surrounding ectoplasm, which regenerates.
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Ape Escape: In the true final battle against Specter (achieved after capturing all apes scattered throughout the game), he is protected by a white energy shield, which the player must strike multiple times to disable before they can actually land a hit on Specter himself. The shield regenerates each time the player actually hits Specter, as well as on its own.
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In the final stage of Pokémon Snap, Mew floats around in a bubble of psychic energy that prevents you from getting a clear picture. You have to hit the bubble a few times with Pokémon Food or Pester Balls in order to knock Mew out of it, then hit her as well to get her to stop chasing after it long enough for you to try and get a decent shot. Then she teleports back into the bubble to start the whole process over again until you reach the end of the stage.
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In Transformers: War for Cybertron Soundwave sends his cassettes to fight while he stays behind an energy barrier.
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 Transformers: War for Cybertron (Video Game)
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Doc Ock in Spider-Man (2000) is protected by a sort of electric field that must be shut off in order to get close to him and do damage.
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A few examples from Devil May Cry series:
Devil May Cry: In the first phase of his boss fight, Mundus periodically summons four magical orbs to create a protective barrier against Dante's attacks.
Devil May Cry 2: Jokatgulm subverts this. You can bypass hacking away at her tentacles and go straight for her head, but it's a lot easier without her tentacles in the way.
Devil May Cry 3: Dante's Awakening:
Cerberus is covered in ice armor over his body that needs to broken through to attack his body parts, which he'll restore after at least one ice covering is fully destroyed with some time.
Leviathan's Heart is encased in a hard shell that opens up for a short time when one of two adjacent organs is destroyed. The other organs recover quickly and you are also constantly swarmed by mooks that make it difficult for you to directly attack the heart.
Nevan has an electrical shield that drops when all of the bats surrounding her are destroyed. And then you must instantly attack her at least once or else she'll immediately regenerate the shield to full.
Devil May Cry 4: Sanctus has a regenerating force field you must destroy to damage him and constantly floats away when you try to close the distance. Overlaps with Tactical Suicide Boss, because the probes that spawn and orbit around him can be grabbed and used to pull yourself towards him - although sometimes he tries to rectify this by making them explode when you're near them.
Devil May Cry 5: Urizen puts up a shield that Nero or Dante must destroy before he can be damaged. After some time, he will regenerate the shield and while it goes down easier, his attacks became more aggressive and hit much harder.
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Pokémon:
A few boss battles from Pokémon Pinball.
In the first game, Mewtwo protects himself from the player's attacks with a ring of rotating psychic orbs; he regenerates them every time the player succeeds in inflicting damage, although as his HP drops, the barrier becomes progressively weaker, allowing more attacks to slip through.
Groudon from Pinball Ruby And Sapphire works similarly, frequently executing a shockwave attack that surrounds himself with pillars of flame that block the player's attacks until they can take at least one of them out.
In the final stage of Pokémon Snap, Mew floats around in a bubble of psychic energy that prevents you from getting a clear picture. You have to hit the bubble a few times with Pokémon Food or Pester Balls in order to knock Mew out of it, then hit her as well to get her to stop chasing after it long enough for you to try and get a decent shot. Then she teleports back into the bubble to start the whole process over again until you reach the end of the stage.
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In the Wii version of Punch-Out!!, King Hippo becomes this kind of opponent in Title Defense. He uses a manhole cover he finds in an urban street to cover his belly during his fight against Little Mac. The cover is attached by three pairs of duct tapes, and to disjoint each pair the player has to stun Hippo after countering an attack and then land three hooks. When the cover is dropped (hitting one of Hippo's feet in the process), then the fight proceeds as a regular one.
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Mega Man X6:
As long as the crystals on Rainy Turtloid's back are intact, the player cannot damage him.
The first Gate's Laboratory boss, the Nightmare Mother, is only vulnerable when their cores move out of the mass to attack.
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In Mega Man X8 the Final Boss' Desperation Attack turns the battle into a Time-Limit Boss. He then protects himself with multiple layers of shielding that must be broken before the player can hurt him again.
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A penultimate boss in Psychonauts uses Telekinesis to protect himself with several rings of debris, and the player must use Raz's own various powers to break holes in each layer and deliver a strike, while the boss is simultaneously using his own psychic powers to repair each breach.
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 Psychonauts (Video Game)
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The Legend of Zelda: Ocarina of Time: Starting with this game, most boss battles typically consist of using a newly-acquired weapon/tool from the latest dungeon to "stun" the boss and expose its weak point to ordinary sword strikes before the boss recovers from it; the entire process is generally repeated three times before the boss dies.
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The Legend of Zelda: A Patra swarm's large central flying eyeball is surrounded by a ring of smaller ones. All of the small eyes need to be defeated before the large one can be taken out.
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Breath of Fire: Dragon Quarter has a variation with the Regents and their "Absolute Defense". From a gameplay standpoint it simply absorbs a set amount of damage from the party's attacks, requiring them to string together Combos long enough to overcome it; but it is visually depicted as a Beehive Barrier absorbing each hit until it shatters.
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Duo of Battle Network 4 is only vulnerable when his Chest Blaster cannon starts glowing red (which is also a tell that Duo's preparing an attack).
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 Mega Man Battle Network 4: Red Sun and Blue Moon (Video Game)
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In TRON, the Master Control Program protected its weak point from Tron by summoning a layer of energy shields; Tron could take out individual shields easily with his disc, but the MCP rotated the shield layer too quickly for Tron to make a successful shot; it was Flynn's Heroic Sacrifice that paralyzed the MCP and allowed Tron to land a clean strike between the shields.
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 TRON
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The MCP. While also being harassed by Sark, Sora has to hack through a barrier, presumably a firewall of some sort, and use a special Action Command with Tron to fire a beam at the MCP's core and delete it. The Updated Re-release also has an Optional Boss fight against Vexen, whose shield needs to be destroyed before he can be damaged directly. Half the fun is just getting close enough to do this while avoiding his attacks and keeping him from scanning you, especially since he reforms the shield if you leave him alone for more than a couple seconds.
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Plants vs. Zombies 2: It's About Time has two:
Frostbite Caves' boss, the Zombot Tuskmaster 10000 BC. Not only is it covered in ice that must be taken down in order to damage the boss, but it will also create columns of ice walls in front of it to block attacks, and these ice walls will spawn zombies when destroyed. If the ice around the boss is destroyed, it will get stunned for a moment, allowing the plants to wail on it before it refreshes the ice (and one column of ice walls).
Neon Mixtape Tour's boss, the Zombot Multi-Stage Masher. It has a column of speakers in front of it that deal gradual damage to plants, and they will periodically flash white before shooting a sonic wave that destroys all plants and zombies in that lane. Thankfully, the Cactus' spikes will deal penetrating damage to hit the boss behind, the Phat Beet will pierce the speakers damage the boss, and the Spore-Shroom's lobbed projectiles will fire over them and hit the boss directly.
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Mario & Luigi: Dream Team:
The Pillodium takes little damage until its two wings have been destroyed, after which it'll drop to the ground and suffer from an attack/defense debuff until its wings have been completely repaired by its bits. This process can be slowed down by attacking the partially repaired wings.
The final boss, Dreamy Bowser, will shield his head if the Bros. try to attack it while his right arm is still functioning. Though you can aim for his body with certain attacks, his head takes significantly more damage. Annoyingly, unlike the previous boss, any amount of healing will make his arm function again, and he can start healing himself whenever he wants to, which also forces you to eliminate a mob of his minions before he'll come back and fight you again...
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In Digital Devil Saga, the last form of the Final Boss Onmyo Harihara is surrounded by six different orbs. Five of the orbs cause her to be impervious to a different element, and the sixth orb reflects physical attacks. You need to strike down the orbs to even start hurting her, but she automatically restores one for free every turn. If you don't have something that does Almighty damage to wipe out all the orbs at once, you're looking at an uphill battle.
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The Emperor Ing in Metroid Prime 2: Echoes provides two examples in one long battle: In its initial form, Samus must destroy its tentacles to expose its weak point for damage; in its final form, hitting its weak point with enough firepower prompts the boss to shield it with either Light or Dark energy, at which point the player can actually damage the boss with the opposite energy weapon.
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Final Fantasy Crystal Chronicles: The Final Boss battle takes place in the sky, with only the boss's tail within attack range. Damaging his tail eventually brings the boss down to your level to strike directly, but only for a limited time.
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Another Metroid 2 Remake has the Tester, a mechanical boss with turrets and two layers of shielding protecting its vulnerable core: four segments of armor plating that are immune to beams but vulnerable to missiles, and an energy shield that is immune to missiles but vulnerable to beams. Each segment of armor will eventually repair itself if not destroyed completely, but the inner energy shield is gone for good once you break it. (Unless you're playing on Hard mode, in which case the energy shield will also regenerate after a short time.)
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Chrono Trigger: In the final battle, you'd think that Lavos's main body is the centre 'pod'. It's not. The right-hand pod is the true core; when it dies, the others do. Thing is, you have to destroy one of the other pods first to get it to lower its defences (all attacks on it are functionally ineffectual otherwise, doing single digit damage) while it tries to resurrect the dead pod.
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G-Darius: You have to destroy Absolute Defender's (regenerating) shield generator in order to damage him, but once you do so, you can hit him anywhere in order to damage him.
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 Darius (Video Game)
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A boss in Super Mario Galaxy, Megaleg, is powered by a Grand Star in a glass dome on its head, and the dome is surrounded by a cage. To beat it, you have to lead a Bullet Bill up to smash open the cage... at which point a spinning wall pops up to protect the dome. Sections of the wall can be destroyed with more Bullet Bills, but after a short time they will regenerate, so you need to lead a Bill though the gap before it closes. Or you can do some fancy jumping to get the Bullet Bill to fly OVER the wall.
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 Super Mario Galaxy (Video Game)
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The BES monsters' main gimmick in the Yu-Gi-Oh! TCG is that they cannot be destroyed by battle, but each one enters the field with a number of counters representing shields. Each time the monster battles, a counter is removed, and if it battles with no counters, it is automatically destroyed.
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The Legend of Zelda: Oracle Games:
In Ages, Pumpkin Head's true form is a small spirit hiding inside the jack-o'-lantern that forms its head. To harm it, Link must first destroy its body and then toss aside the Jack-o'-Lantern to reveal the spirit, then strike at it while it dashes back to the lantern. Pumpkin Head then reforms its body, and the process repeats several more times to defeat it.
In Ages, Eyesoar's central eye is protected by four smaller eyeballs orbiting around it. Link must shoot the Switch Hook into a gap between the eyeballs in order to stun the central eye, which will cause its entourage to scatter and leave it vulnerable to attack until they re-gather.
In Seasons, Manhandla's weak point is a red core within its body. To defeat it, Link must first destroy its maws and then break through its armor with the Magic Boomerang, after which he will only have a short time to attack the core before Manhandla's body regenerates.
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The final boss of Dark Messiah summons a skeletal dragon to fight you while he remains in an indestructible forcefield. Killing the dragon makes him lose the shield for a few seconds; then he summons another one, rinse and repeat.
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In Mega Man Zero 4, Zero can't deal any damage to the Final Boss as long as the spike shield between them is up. The boss only lowers his shield when he's about to attack.
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In Paper Mario: The Thousand-Year Door, the Yux enemies can generate Mini-Yux from themselves, which produce shields that can block all damage Mario and his partners can do. The regular and "Z" Yuxes create one mini-Yux per turn, meaning Mario or his active partner can destroy the Mini-Yux while the other harms the Yux directly. The X-Yux, however, generates two per turn, requiring multi-target attacks, or else the X-yux will just create another shield as soon as the last one goes down. Grodus, the Mad Scientist who created these enemies, uses a similar system in battle, where he'll summon two Grodus X units per turn. Each Grodus X reduces damage to Grodus until four of them surround him, upon which they will negate all damage done to Grodus until at least one Grodus X unit is destroyed.
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In Mega Man 7, a giant pumpkin Mini-Boss in Shade Man's level is modeled after a Russian nesting doll, with a small component being shielded by two outer layers. However, as a slight subversion, the Pumpkin can be destroyed in two different methods, one of which doesn't involve even touching its core; just concentrate fire on the outer layer.
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Mario & Luigi: Bowser's Inside Story:
The giant Wiggler. It can only be damaged in the head after all its segments have been turned yellow (you do so by attacking the segments), but it will turn back to red in a short while, forcing you to repeat the process.
The final boss follows in the footsteps of the previous games, but has Bowser fight against Dark Bowser until he knocks the Dark Star Core/Fawful out of him, after which he needs to vacuum it up so the bros. can fight it. This in turn requires them to first destroy both of its glasses' lens so they can destroy its three legs (As the boss simply retract them if the Bros. attack while he can see clearly), then they can finally attack the core and deal some lasting damage. Failure to destroy it in a few turns requires you to repeat the entire sequence beginning from Bowser's part, but thankfully, its HP isn't that high.
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A few boss battles from Pokémon Pinball.
In the first game, Mewtwo protects himself from the player's attacks with a ring of rotating psychic orbs; he regenerates them every time the player succeeds in inflicting damage, although as his HP drops, the barrier becomes progressively weaker, allowing more attacks to slip through.
Groudon from Pinball Ruby And Sapphire works similarly, frequently executing a shockwave attack that surrounds himself with pillars of flame that block the player's attacks until they can take at least one of them out.
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Mario & Luigi: Partners in Time: Princess Shroob attacks the brothers on a mechanical throne with a Deflector Shield protecting her. You have to destroy the shield (which notably takes a fixed number of hits regardless of damage), disabling the throne and forcing her to fight on foot, before you can damage her directly. The second fight against the elder Princess Shroob extends this pattern one step further: you cannot damage her until you've destroyed her crown, but you can't strike the crown without attacking her feet to knock her down first. In both cases, the princess recovers after a short while, forcing you to start the process over.
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Mega Man Battle Network:
Like the Devil series, Alpha's core from Battle Network 3 is open to attack once you tear open its gelatinous shell with rapid-fire attacks.
Duo of Battle Network 4 is only vulnerable when his Chest Blaster cannon starts glowing red (which is also a tell that Duo's preparing an attack).
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The Goronzoran from from Phantasy Star Online 2 is an extremely fat humanoid dragon who rides in a hoverchair, shielded by a magical barrier. The barrier can be removed by destroying the four crystals that orbit around it, after which you'll get a short period of time to freely attack the boss while he struggles to get his chair floating again.
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The final boss of System Shock 2 is against SHODAN in cyberspace, where she has an MCP-like shield around her head that has to be disabled by hacking terminals in the arena. She can also fire at you through the shield, summon holographic minions to attack you from the sides, and can even make parts of the floor hurt you. Depending on what weapons and skills you have, the fight can range from That One Boss to Anti-Climax Boss.
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Mega Man:
The franchise-wide Recurring Boss Devils can only be attacked when their eye/core is open. The Green Devil of Mega Man 8 and Mega Man & Bass takes it a step further — not only is it only vulnerable while its eye is open, its eye is held in the center of its body, which must be pushed out of the way by shooting at it before you can even reach the eye.
In Mega Man 7, a giant pumpkin Mini-Boss in Shade Man's level is modeled after a Russian nesting doll, with a small component being shielded by two outer layers. However, as a slight subversion, the Pumpkin can be destroyed in two different methods, one of which doesn't involve even touching its core; just concentrate fire on the outer layer.
Mega Man X6:
As long as the crystals on Rainy Turtloid's back are intact, the player cannot damage him.
The first Gate's Laboratory boss, the Nightmare Mother, is only vulnerable when their cores move out of the mass to attack.
In Mega Man X8 the Final Boss' Desperation Attack turns the battle into a Time-Limit Boss. He then protects himself with multiple layers of shielding that must be broken before the player can hurt him again.
In Mega Man Zero 4, Zero can't deal any damage to the Final Boss as long as the spike shield between them is up. The boss only lowers his shield when he's about to attack.
For the Final Boss of Mega Man ZX Advent, you have to damage his forcefield enough for it to disappear, then quickly get your hits in before it gets back up again. He takes it even further than most by having two different movesets depending on whether the forcefield is up or not.
Mega Man Battle Network:
Like the Devil series, Alpha's core from Battle Network 3 is open to attack once you tear open its gelatinous shell with rapid-fire attacks.
Duo of Battle Network 4 is only vulnerable when his Chest Blaster cannon starts glowing red (which is also a tell that Duo's preparing an attack).
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BoxxyQuest: The Gathering Storm has the Obligatory Kraken Boss and its tentacles. You have to kill them all to make the head surface for a few turns, until the tentacles regenerate. There’s also One_Wing, who occasionally summons a shield of “Underwings� to surround him while he heals.
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Kingdom Hearts:
The desert Optional Boss "Kurt Zisa" in Kingdom Hearts only takes damage when he is stunned, but to stun him you have to attack and defeat the spells he's cast in battle first. Complicating matters is that each time his barrier is defeated he alternates to another attack pattern: One where he casts Silence on your party and attacks exclusively with his massive swords, and another where he's protected from physical attacks by a magic barrier and attacks exclusively via magic.
Kingdom Hearts II:
The MCP. While also being harassed by Sark, Sora has to hack through a barrier, presumably a firewall of some sort, and use a special Action Command with Tron to fire a beam at the MCP's core and delete it. The Updated Re-release also has an Optional Boss fight against Vexen, whose shield needs to be destroyed before he can be damaged directly. Half the fun is just getting close enough to do this while avoiding his attacks and keeping him from scanning you, especially since he reforms the shield if you leave him alone for more than a couple seconds.
The Updated Re-release includes an Optional Boss fight against Vexen, whose shield needs to be destroyed before his actual health can be damaged. He'll also respawn his shield in he isn't attacked right after it breaks. Naturally, this also applies to his data battle.
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Hollow Knight: You cannot damage Uumuu directly without popping its outer jellyfish layer and exposing its core first, something that can only be done via external means. In the main storyline, Quirrel joins the battle in the Teacher's Archives to pop it with his weapon. In Godhome, you instead need to play aggro with the Oomas and use their explosions to target Uumuu. In both cases, Uumuu will restore its protection after a few seconds, requiring the process to be repeated several times.
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Mario & Luigi: Superstar Saga:
In the rematch against Fawful, he starts off hiding in an invention of his that's completely impervious to damage. However, landing enough hits will provoke him into using a powerful attack that overheats the machine, forcing him to leave it temporarily and make himself vulnerable.
When facing the Final Boss, you must destroy its hands and head in order to expose (and strike) its heart; the hands and head quickly regenerate, requiring you to repeat this process throughout the battle.
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The gigantic war golem Mogenar in Metroid Prime 3: Corruption has four Phazon cores (in various locations) shielded by red energy orbs; the player must blast through the shielding and then deliver a strike at the core with their Hyper Beam. Mogenar can regenerate the energy orbs using fixtures located along the edge of its Boss Room, and regenerates all of them whenever any core is destroyed. It is considered one of the game's most difficult battles.
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Boss Battle
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Older Than the NES
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