Fugo was written out of JoJo's Bizarre Adventure Part 5 because his ability was essentially "kill the enemy in half a minute". Needless to say, battles would be a lot less interesting if they were all won by unleashing a killer virus on the enemy that kills them quicker than tying your shoes.
Near the end of Neon Genesis Evangelion, Eva Unit 01 had become so powerful (thanks to a Mid Series Upgrade) that it was usually written out of the episodes in order to avoid ending the battles too quickly.
The third Rebuild of Evangelion movie does this as well, since Unit 01 had essentially become a god at the end of the second film. The Eva is used to provide perpetual power for Misato's Cool Airship, the Wunder, and Shinji ends up piloting Eva Unit 13 instead.
In the second Naruto movie, Gaara develops a sudden case of never-there-on-time and thus is constantly busy being late while everyone else fights their last, easily squishable battles.
Claire Stanfield of Baccano! isn't quite written out of the light novels, so much as Wordof God has stated he'll never get his own story arc or book since he'd just solo the entire cast in under thirty pages.
In Slayers, the ridiculously powerful Xellos always seems to disappear at the most inconvenient times...or, even worse, is deliberately unhelpful. This is initially justified by his apparently flighty and unreliable personality, and later even more justified by the revelation that he is actually a very loyal and reliable agent...to the other side. Likewise he can only be as helpful as he wishes as long as he doesn't arouse suspicion.
That and Xellos just really enjoys dicking people around.
Goku, despite being the hero, often plays this role in Dragon Ball, particularly the early seasons of Dragon Ball Z. Since he'll almost inevitably win the battle once he joins in, circumstances always conspire to keep Goku on the sidelines just long enough for all the other heroes to get beaten up first. When Vegeta and Nappa arrive on Earth, he's still in the afterlife and is only revived once all the others have been thoroughly defeated. When everyone goes to Namek, his spaceship's the last to arrive, and soon after landing, he's critically injured and spends several more episodes floating in a regenerative tank. When Doctor Gero begins his rampage, Goku's too busy fighting off a heart illness to help. And so on...
In fact, Dragon Ball Z distinguishes itself for having multiple tiers of the trope - a really long fight will probably start with Yamcha or Krillin, then bring in The Worf Barrage of Tenshinhan/Piccolo/Trunks/Vegeta, and finally let Goku or Gohan show up to finish things...and at least one fight (versus Cell) takes this even further, for a grand total of eight fighters in sequence facing off against him in a row, without any other villains participating. Naturally there were very good, impressively coincidental reasons they couldn't all have attacked at once.
Vegeta gets the "honor" of doing this on the second Broly movie. There's zero reason as to why he didn't rush in the instant he detected Broly's ki (And he should have detected it), and at this point in the timeline, Vegeta had Super Saiyan 2, which could have trounced the pile of muscles easily (Or at least be actually helpful, as long he didn't Forgot About His Powers like Gohan who didn't go beyond regular Super Saiyan).
This trope is the entire reason why Vegetto de-fused once he entered Buu's guts. He outclassed him so much that the fight wouldn't have had ANY tension whatsoever if Vegetto finished it. Also, GT would've never happened.
This is also the same reason why Gohan, Goten, and Trunks were killed by Buu when he destroyed the Earth while they were still unconscious. Gohan and Gotenks outclassed the de-powered Buu so much that there would be no tension in their battle. This is lampshaded, as Goku suggests bringing them in to destroy Buu after they are revived, but Vegeta refuses because he wants the people of Earth to protect themselves.
In the Skypiea arc of One Piece, Luffy spent most of his time inside of a giant snake. He broke out just when every other bad guy was defeated except for Eneru, the villain of the arc. It wasn't that he was overwhelmingly powerful at the time compared to his crewmates, just that due to his rubber body he was completely immune to most of what Eneru could do and was capable of taking him out pretty easily compared to other big bads. Super-Effective indeed.
This happens a lot to Luffy. While his True Companions are busy fighting the underlings of the Big Bad, he's usually trapped in a block of concrete or wandering secret passages looking for the Big Bad. A quick rundown: Stuck in a cage, running off in the wrong direction and later hit with a sleeping spell, defending a restaurant (actually a major event), trapped in said block of concrete and underwater, well-fed and sleeping, trapped under a mountain, Not Quite Dead and buried, eaten by a snake, it wasn't his turn yet, trapped between buildings (twice), on a different train, charging in alone, wandering secret passages, and lost in a forest.
Red Haired Shanks, during Whitebeard's war on the World Government was busy battling another of the Four Emperors.
Earlier in the series, when Luffy's brother Ace was first introduced, he proved be an extremely powerful combatant, easily destroying a fleet of ships with a single attack, and fighting a previous logia antagonist to a standstill. Said logia curbstomped Luffy during their first meeting. He was probably one of the strongest characters in the entire SAGA. While it's clear that he's much stronger than Luffy, especially with his logia abilities, he doesn't bother getting involved in the whole Arabasta affair. He is a pirate, after all. And he was looking for Blackbeard.
This happens to the entire crew so that Luffy can go and try to save his older brother from his execution.
Since every One Piece arc ends with Luffy beating the strongest Arc Villain, this trope also happens to Zoro, who is just as strong as Luffy, to prevent him from taking Luffy's kill. Sometimes Zoro just happens to be at another place than Luffy, but it usually happens this way: Zoro gets some handicap (like a wound or missing swords) that severely halts his fighting ability. Zoro insists to fight anyway and challenges the villain's Dragon or strongest henchman. Zoro wins with lots of difficulty due to the handicap (without the handicap, he would probably win easily). Zoro is now so exhausted that he cannot handle the main villain, so it's all up to Luffy.
Bleach has done this with Ichigo, who usually is undergoing training or otherwise distracted while Uryu, Orhime, and Chad fight minor characters.
An anime filler arc has the main villain freeing the spirits of the Zanpakuto to fight against the Shinigami. When Yamamoto's Ryuujin Jakka refused to rebel, the Big Bad seals Yamamoto in some sort of barrier, leaving him MIA thus far.
Turns out, Yamamoto sealed himself in there in order to keep Muramasa from accessing his memories. Making this a subversion of sorts.
Small fry. Every single major event in the series relies upon single combat, usually involving Ichigo, however much/little sense this makes. The lengths the story goes to in order to justify things such as the three strongest Captains (including Yamamoto, naturally) all being out of play when the Big Bad first appears, or a group of only five people (out of the twenty or so at the right power level) going into Hueco Mundo are generally amusing, but eventually, the show stops even giving explanations (why, exactly, did Urahara's group wait so long to join the False Karrakura Town battle?) and calls it a day.
In Pokémon Special, main character Red is frozen in a block of ice so that Yellow can take over in the second story arc.
In Pokémon, meanwhile, Ash routinely gets rid of his old high level Pokemon to make room for the new models.
This is actually played with in the early Johto episodes. Ash has Charizard with him for a while and uses him to absolutely obliterate every single trainer he comes across, most of which are just starting out. Brock and Misty call him out on this.
Ash also has a tendency in full battles to lose or not be carrying a mon that would have an advantage over his enemy's ace. This practice actually began with Lapras getting double koed in his battle with Drake, whos Dragonite has a weakness to ice.
Done occasionally in Mahou Sensei Negima!. During the Mahora arc, Negi had to go off and find the Big Bad, leaving everyone else to take care of her army of robots. Later on, during the Gateport incident, Fate incapacitates Negi by impaling him with a chunk of rock, forcing his True Companions to fend for themselves until Negi recovers. Another possible example would be Konoka, who's an unstoppable force of healing with an inextinguishable pool of Mana, but rarely arrives to the battle till she's not needed, leaving her to handle clean-up instead.
Another example of this combined with Too Powerful to Live: Jack Rakan, who was essentially invincible, is ultimately defeated due to Fate's newly revealed Reality Warper abilities. Granted, there's a good plot reason for Fate to have that power, but it seems to have been revealed solely to have an excuse to take out Rakan.
A third example is Evangeline. A vampire and one of the strongest mages in the manga, she easily wipes the floor with Fate when the two encounter one another. However, due to the fact that she's stuck within Mahora Academy grounds, she can't help Negi and his friends when they need her. When she finally gets a chance to join the final battle, it's over very, very quickly.
In Digimon Frontier, a new enemy called IceDevimon appears and "freezes" The Hero's and The Lancer's Transformation Trinkets, saying he'll save them for later. "Later" never comes, because while he's got a few flashy tricks for a Champion-stage Digimon the rest of the gang is able to defeat him within that episode instead of after a miniarc. It was the last time any of the supporting characters got to do anything for the rest of the series, and it occurred halfway through, after which the Spotlight-Stealing Squad of Kouji and Takuya literally took away the other's powers to fuel their super modes.
Seraphimon also appears within the first ten episodes, the earliest we've ever seen a Mega Digimon. He gets The Worf Effect so that he doesn't wrap up the plot easily.
Its done earlier in Digimon Adventure. Patamon is always the last to digivolve to new levels, so that the other Chosen have the chance to fight. When he first becomes Angemon, he one-shots Devimon, (though it requires a Heroic Sacrifice that prevents him from digivolving again until conveniently much later in the series), later Phantomon, and even holds off Piedmon briefly in melee combat. He doesn't get his ultimate stage until the first of the final three episodes, and THAT stage has virtually an instant-ko as an attack.
The following season has the previous chosen give up the power to digivolve beyond the Champion level, so that they don't Curb-Stomp Battle all enemies and outshine the new children
In YuYu Hakusho, Yusuke sleeps through much of the preliminaries of the Dark Tournament, and only wakes up just before his fight with Chu. In the second round, Hiei and Kurama spend the entire round fighting a giant robot, which prevents them from getting to the stadium. In round three, Hiei and Genkai are tricked into agreeing to take a medical examination, then trapped in a force field for the duration of the round. Yusuke is unable to fight in the semifinals because he is in the extremely painful process of acquiring Genkai's power, and falls asleep after that. And Genkai is unable to fight in the finals, due to being dead.
Not really this trope though outside of Yusuke during the semifinals (and possibly Genkai during the finals) as all members of team Urameshi, save Genkai, were of comparable strength throughout the tournament and all this did was lead to more endurance matches as fighters had to complete multiple rounds.
Hellsing does this to Alucard, having him trapped on a boat whilst London is attacked. Which was The Major's plan all along.
Striker S Sound Stage X revealed that all the insanely powerful series veterans were too busy with their own missions to help with the current incident, giving the Strikers and reformedNumbers Cyborgs a chance to really strut their stuff and save the day.
Previously in Magical Girl Lyrical Nanoha StrikerS, Nanoha, Fate and Hayate, the three most powerful protagonists, attend a press conference where they are not allowed to carry their Intelligent Devices. Unfortunately, Scaglietti's Numbers and other allies attack during the conference, and by the time Nanoha, Fate and Hayate receive their devices, they're too late to make much of a difference.
Fox Spirit Chizuru is Brought Down to Normal prior to a major battle in Kanokon, giving Ordinary High-School Student Kouta the chance to defeat The Dragon by himself. It's a bit of an unusual example, because normally they work together anyway to defeat their enemies, but Chizuru usually prompts their fusion and she's in control during it, and Kouta still needed her around so he could possess her (usually it's the other way around) during the fight, but he still does the work himself.
The author of Rurouni Kenshin specifically stated that Sejuro Hiko, Kenshin's master was so powerful that he was an unfair advantage for the heroes. His sidelining is mostly due to the character's own disinterest in the heroes' struggles, so he only comes in to help rarely, rather than being plot-deviced out. He's just not that heroic.
Miroku of InuYasha has a powerful attack called the Wind Tunnel, which can suck anything into a void. This is anything, so in his debut appearance when he is opposing the eponymous character, he issues a warning to villagers to put some distance from him, leading to his Defeat Means Friendship. In addition, if he sucks in anything poisonous, he gets poisoned, and Naraku has plenty of poisonous wasps to give as support. Also, overuse and even having the ability at all for too long will eventually lead to his death.
You can almost sense that the author regrets giving Miroku such a powerful ability in the first place. After a certain point in the series, EVERY battle includes a token scene where Miroku tries to use Wind Tunnel only to have Naraku's poison bees show up out of nowhere, preventing him from using it. This has the ironic side-effect of making him the most powerful character on paper, but the most useless in practice.
In Muhyo And Roji, Page sets up Training from Hell for Roji and other magic law practitioners by locking them in a house and sending real haunts after them. Unfortunately, one particularly dangerous haunt, Bellocent of Mist Mountain, sneaks into the test and cuts the power, preventing Page and the other powerful magical law practitioners outside from opening the gates when they realize that the test has become far more dangerous than it should be, and they only get in after Roji has already won.
Rave Master's Elie could have easily used her magic to wipe Demon Card off the map, blow Lucia into the next century (maybe even literally given how she blew herself half a century forward) and cream Doryu and Ogre, which would have kept Hardner from ever attempting his fusion gambit. Naturally, she had to go and get amnesia so she wouldn't know how to do all this.
Happens again when Laxus and his bodyguards try to take over the guild, and Makarov, Natsu, and Gajeel are prevented from doing anything because a a barrier is keeping them sealed in one area of the plaza.
This happens to Erza in both the Laxus story arc (turned into stone, until her magic eye makes the spell run out early) and the Oracion Seis arc (poisoned by Cobra and left disabled until the other members could rescue Wendy who could cure the poison).
This actually happens in nearly every major arc, with Erza being the primary target (which makes sense, because given Laxus' lazy/disinterested nature and Mystogan and Gildart's near constant absences she is essentially the strongest member of the guild who's available to help). Lets see here...
Phantom Lord Arc: Makarov as stated above, and Erza is KO'd after tanking a shot from the PL massive cannon so nobody else got hurt. Laxus refuses to help, And Gildarts is still off on his 100-year Mission while Mystogan is busy getting Makarov his magic back
Tower of Heaven Arc: Erza is stuck inside a card (meant to protect her, ironically) until the battle with the Big Bad's Dragon Swordmistress and the Big Bad himself.
Fighting Festival, see above. Plus, during the Final Battle, Mystogan leads off and appears to have the upper hand, but gets his mask blown away revealing his identity as the Edolas Jellal, which means their faces are identical and he leaves to avoid causing a rupture with Erza and Natsu, THEN Erza leaves the building to lead the counterattack against the Thunder Palace before it wrecked the town, leaving Natsu and Gajeel to handle the arc's Big Bad.
Oracion Seis Arc: See above. Also, A resurrected Jellal is taken out of the action early against Midnight and later can only support Natsu by giving him the Flame of Rebuke, as the Midnight battle left him too drained to fight.
Edolas Arc: Practically the entire set of heavy hitters in the Guild is taken out of the way by being frozen as a lacrima crystal. However, this is a noticeable aversion for the series, because Erza is NOT among them this time, although much of her time is spent locked in combat with her Edolas counterpart.
Grimoire Heart Arc: Makarov is taken out early by Hades, and Gildarts, Fried and Bickslow all left the island before the attack begins. They do return later, however.
Juvia is also a frequent victim since unlike most of the guild she's actually friends with most of Natsu's team, and doesn't have her own team to hang with. Despite this she's rarely tagging along with Natsu's group, and when she is she's usually disabled by either stone/taking herself out to free another/frozen in Lacrima. This is because (much like the Logia users in One Piece) she can ignore most attacks by turning her body into water and reforming so most enemies can't hurt her. The two times she did assist them in battle she was brainwashed for most of the first fight until Lucy freed her so they could double team the villain, and the other was against an opponent who could negate her water shifting by causing her pain and damage regardless.
Speaking of Laxus, in what sadly appears to be a Redemption Equals Affliction scenario due to him having performed a Heel-Face Turn, at the beginning of the Tartarus arc he and the entire Thunder God Tribe are out of commission after the demon Tempesta pulls a Taking You with Me by releasing a deadly poison into the air with the intention of killing off the entire town of Hargeon, and Laxus himself makes a Heroic Sacrifice by inhaling as much of the poison as possible in a desperate bid to save the town's citizens. He survives, but just barely, and the poison still manages to kill over a hundred Hargeon inhabitants.
Happens all the time in all the story arcs of Saint Seiya with Ikki. The Phoenix has the "Strength of an army" but is always elsewhere. Mildly applied to Shiryu as well, but...well, he's not as strong.
Happens in the second episode of Yu-Gi-Oh!. It seems the author realized that having Yugi beat Kaiba at the end of the first card game arc (pilot episode in the anime) by using Exodia, the only invincible, instant win monster in the entire game, was a problem now that the entire series became about this card game. After all, every conflict would become a preordained conclusion; if Yugi's about to lose he will draw Exodia and get the instant win. So immediately after that (the second damn episode in the anime) they get thrown off a boat by a minor character and never brought up again.
They actually do in the alternate form of Exodia Necross and the Rare Hunter who builds an illegal deck around drawing Exodia, and said minor character (Insector Haga/Weevil) is Yugi's first Duelist Kingdom opponent.
In HeartCatch Pretty Cure!, there's Yuri Tsukikage, alias Cure Moonlight, who's taken out in the very first episode and left powerless for 3/4ths of the series. Once she regains her powers, you can clearly see why she was taken out.
There's also the mysterious man who saves Tsubomi from time to time whose actually her grandmother's fairy partner, Coupe. He just shows up to rescue the girls and bails out quickly.
A minor example in the "Little Army" prequel manga for Girls und Panzer. When Miho is hiding in a tank while burdened with doubts over whether to continue with tankery, just as Emi is set to leave for Germany, Sakuyo, one of the family maids, makes note of her habit of doing this whenever she's troubled, but then thinks to herself that it was always her sister Maho who convinced her to come out. The task of persuading Miho to come out falls to Sakuyo and Miho's friends, Chihiro and Emi.
This is the main reason why in Queen's Blade RebellionLeina, the main heroine, is sidelined for almost the entire story: By the time Rebellion came out, Leina becomes the most powerful living being (only behind the angels and demons) ever existed, being able to wipe out armies by herself. The only way to make Leina not taking part of the plot of Rebellion is by making The Swamp Witch cursing her by making her sleep for many hours and hindering her skills, so Leina could not being able to steal the spotlight from Annelotte and the rest of the new cast.
Partway through Watchmen, Ozymandias gives a bunch of people cancer and tricks nigh-omnipotent Dr. Manhattan into thinking he caused it, prompting him to take a vacation on Mars. Doc comes back for the finale, but doesn't arrive until after the villain's plan has been carried out.
In the 1960s, when Adventure Comics featured the Legion of Super-Heroes, the Legion had several one-off encounters with some guest character (often a stranger applying for Legion membership) who harbored a secret, and who often turned out to be (in disguise) someone whom the Legion already knew. In each of these stories, Saturn Girl was conveniently called away on some separate emergency and wasn't able to participate in the main adventure. Saturn Girl is a telepath: if she had been available to read the stranger's mind, the story would've ended on the first page.
This is practically the raison d'etre for Marvel Comics superhero The Sentry. He's a throwback to heroes (well, okay, mostly just Superman) from the Silver Age, with all that entails; he has "the power of a million exploding suns" and is recognized as pretty much hands-down the strongest super in the world. And he could handle pretty much any threat that emerged with one hand tied behind his back... if it weren't for the agoraphobia and super-evil split personality that incapacitates him whenever he'd be most useful.
During the early issues of The Defenders (Marvel Comics, we're going off the original series here), the writers had trouble coming up with halfway decent reasons why Doctor Strange couldn't just wave his hand and eliminate the problem in one page.
Strange also took himself out of the story for forty days during Civil War, claiming it wasn't a matter for the office of Sorcerer Supreme. He later regretted his inaction.
Just about all Transformers comic book universes have done this with Optimus Prime at least once. Often the autobots will splinter into groups without their leader. If Megatron is also missing because Prime performed a Heroic Sacrifice and sent them both to another dimension, the Decepticons will be just as lost.
Professor Xavier also tends to suffer this fate as, at his full potential, he should be able to just sense and mindwipe any sentient problem that's heading the X-Men's way. Hence, most major threats in the X-Men comic books will begin with Xavier either disappearing, losing his powers, falling into a coma, turning evil, or otherwise being rendered useless for the rest of the story. In the movie trilogy, Xavier spends at least half of each film out of commission, so the other characters will have to fight the battle. You might as well call having this power the Charles Xavier Superpower.
In X-Men, the answer to The Sentry is one Nate Grey. The alternate version of Cable, without the techno-organic infection it takes the constant occupation of the bulk of Cable's powers to repel, is a very powerful telekinetic and telepath. He underwent Power Creep, Power Seep, and returned after an absence even stronger, so for a while was as strong as Jean in full Phoenix mode, all the time, without any of the drawbacks. Lately, he burned out his powers opening a dimensional portal, and is down to just telekinesis (how strong remains to be seen.)
Happened to the original Cable, too. He got rid of the technovirus, levitated an entire island while battling the Silver Surfer at once, burned himself out doing so, and was left with limited powers. Now the technovirus is Not Quite Dead and even those powers are reduced by the need to once again play Sealed Evil in a Duel.
For a while, Time Travel had brought Franklin to adulthood. Naturally, this was conveniently reversed right before the OnslaughtCrisis Crossover started, reverting him to childhood so that he could be a power source to Onslaught instead of a threat.
From DC Comics: So there were American superheroes in the 1940s, right? But having superheroes involved in World War II would be a Game Breaker that would disrupt the idea of the DC universe's similarity to the real world. So the Justice Society and their fellow patriotic heroes took a major Deus Exit Machina during World War II. The canon explanation is Hitler using the Spear of Destiny to mind-control any superhero who got too close to Europe, and Hideki Tojo using the Holy Grail to do the same thing with Japan; an Elseworlds tale instead had the heroes at the mercy of a Power Nullifier named Parsifal.
There was a Superman story published during World War II in which Superman told thousands of cheering GIs: "You fellows don't need my help!" This was of course to explain why Superman didn't end the war in five seconds. And of course, during the Golden Age, Superman's powers were much weaker than they were later on: it's possible that he wasn't even able to fly across the Atlantic.
In the early days of the comic, Jerry Siegel and Joe Shuster actually did do a three-page story called "What If Superman Ended the War?" He flies to Germany, grabs Hitler, then flies to Russia, grabs Stalin, ("Joe, meet Adolph!"), and then, with one tyrant in each hand, flies them both to a war crimes tribunal. The end!
Yet another Superman example: There was a much-hyped JLA story arc by Chris Claremont and John Byrne. Superman gets sidelined in the very first issue, and stays that way pretty much throughout the arc. Since it was Claremont, Superman was (of course) sidelined through Mind Control.
In Super Dinosaur Tricerachops is laid up and The Exile is preoccupied during Maximus' Project X.
In the Belgium comic book series Suske en Wiske (Spike & Suzy) , this frequently happens to Jerom because his superhuman strength would otherwise make the situations the characters encounter less of a challenge.
Done multiple times in Marvel Comics. The Fantastic Four are usually in space or another dimension while The Avengers are on a mission. They really should coordinate this. Spider-Man has noted that 99 times out of 100, when he goes to ask another hero for help, they will never be there. Doctor Strange's servant, Wong, replied that this was true, but so far, Spidey was good enough to not really need that help.
In the Johan and Peewit adventure "La Guerre des sept fontaines" the entire motivation of the heroes is to liberate a ghost who has been forced by his forefathers to haunt his old castle every single night until some specific requirements has been met. At one point, the characters actually need his help, but it turns out that the forefathers has unfortunately decided to give him a few nights of respite from his haunting right then.
Superior Spider-Man has this in spades as Doc Ock knows that one smart person or a powerful telepath is enough to blow his cover. Sure enough, thanks to events like Avengers vs. X-Men, a number of brainier people and a number of telepaths are out of the picture.
Speaking of Avengers vs. X-Men, this was one of the major in-story reasoning for the X-Men (or rather, "the mutants defending Hope", since about 1/4 of the then-active X-Men sided with the Avengers) to MAJORLY call the Avengers to task: while the team was able to show up to stop every Tom, Dick and Harry in a super-suit from robbing a bank or instigating a small war, they were "somehow" never around while hundreds, thousands or millions of mutants went through everything from slavery to genetic experiments to genocide or even worse without intervention. There needed to be some SERIOUS Kick the Dog moments after a talk like that to make the Avengers sympathetic again.
Rachel Grey's disappearance from Avengers vs. X-Men is also a point of contention. As the only Phoenix Force host still alive with actual experience, her presence could have easily prevented the event from getting as bad as it did.
Underworld Unleashed runs with this: Neron seeks to obtain the purest of souls and immediately everyone assumes Superman. However, he's not there and many people think Superman was captured by Neron already. This wasn't the case: he was captured by off-world aliens and dragged through "The Trial of Superman" storyline, taking him, Superboy, Supergirl and Steel with him.
The Mighty Thor from Marvel Comics has Odin, King of Asgard, and stated at times to be as powerful as all of the thousands or more of other gods in Asgard including Thor combined. At his lowest he is casually manhandling Thor and at his peak he is remaking galaxies. So of course whenever Asgard is threatened Odin is conveniently in the Odinsleep replenishing his powers, weakened, or missing. The few times he does fight are when it is against a threat that can match him in power...making the rest of Asgard virtually useless.
In Boys Do Tankary, the boys in their new tank could have easily defeated St. Gloriana, but choose to hold back in order to test Miho and the others' abilities, and ensure that they don't end up relying on them.
In Boys Und Sensha-do, as a result of an accident, Miho, the main character is no longer able to serve as team commander at Oarai, forcing Momo, who is her vice captain, in spite of her impulsiveness and short temper, to do it instead.
Master Oogway in Kung Fu Panda, who had previously defeated Tai Lung, Ascends to a Higher Plane of Existence to keep him from doing so again. The in-universe explanation is that he needed Shifu to take over and help Po become the Dragon Warrior, which he wouldn't have done if he kept relying on Oogway. It also strongly implies that it is simply Oogway's time to die, having lived for over a thousand years.
Films — Live-Action
The Matrix franchise usually need to keep Neo away from the action after becoming the godlike One to maintain enough tension.
In The Matrix Reloaded, a backdoor traps Neo hundreds of miles away while Trinity and Morpheus fight the Nigh Invulnerable Twins, then Agents for the duration of the long highway scene.
In Dogma, God is unavailable, since he went to play ski ball and was incapacitated while doing so. While this is going on, two angels banned from Heaven find a loophole that allows them to return to Heaven. Doing so would be against God's word and would destroy the universe. So, Deus Exit Machina (or Have You Seen My God?) drives the movie.
This happens several times in The Karate Kid Part II and The Karate Kid Part III. Mr. Miyagi is able to easily defeat any adversary, so of course for Daniel to have fights of his own, Mr. Miyagi must be away or kept out of the fight for some reason. Most notably is probably the final confrontation in the second movie when the main antagonist drops the bridge into the water, leaving him isolated with Daniel and Kumiko while Mr. Miyagi is only able to watch the Fight To The Death that ensues.
In Dark of the Moon Prime is inexplicably elsewhere when all the other Autobots are trying to guard Sentinel from the Cons. So when Sentinel suddenly turns on them, nobody around is capable of stopping him as he rampages through the base. By the time Optimus finally gets there the base is destroyed and Sentinel is long gone taking his space bridge tech with him.
Done very nicely in Deliverance, where the macho outdoorsman Lewis suffers a gruesome leg fracture, forcing the more relatable character Ed into the hero role for the climax.
In all three X-Men films, Professor Xavier is conveniently done away with before he can just use his telepathy to shut down the mind of the Big Bad (which he is more willing to do, unlike his comic book counterpart). Each film tosses him out earlier than the previous one; the 3rd film kills him off outright until he gets better after the end credits and in X-Men Origins: Wolverine, he simply isn't present to have any impact on the main plot until the end when he guides the mutant escapees to safety with no explanation for why he's just showing up at that point. X-Men: First Class approaches it differently; Sebastian Shaw has a telepathy-blocking helmet that protects him from Xavier from the start; at the climax, Erik steals the helmet, Xavier freezes Shaw's mind, Erik kills Shaw and declares himself the Big Bad. With Charles helpless to stop him, the two part ways to kick start the X-Men film franchise.
In X-Men: Days of Future Past, Quicksilver EASILY takes out the guards in Magneto's prison, and is faster than anybody, even two powerful mutants—and one with enhanced senses—can react. Combining him with Xavier in locating either Trask or Mystique would've wrapped the plot up in far shorter time and at least half the damage. So naturally, he's out of the story once the break-out scene is over, save for a cameo near the end. Justified in that he only worked with the Mutants because of the opportunity to pull off the heist of a lifetime (and Charles probably didn't want to drag more young people into this war after what happened to his students).
Thor has Odin, who goes to sleep for most of the movie, something he periodically has to do to rejuvenate his powers.
Supergirl. A radio news report mentions Superman's departure from Earth on an intergalactic peacekeeping mission, which explains why he isn't around to handle Serena.
In Sky High, Will Stronghold is forced to handle the Big Bad when his parents, expert super-heroes and saviors of the world, are turned into babies by Royal Pain.
The Avengers has several:
Thanks to the destruction of the bifrost, Odin can't come to Earth to clean up after Loki, only having enough dark energy to send Thor.
The Hulk is dropped out of the helicarrier before the final battle, so the others can try to fight the alien army without the unstoppable Hulk until he shows up.
After The Avengers, many fans have wondered how the Marvel Cinematic Universe will explain why the heroes' teammates did not show up in their solo movies to help. So far, we have these reasons:
In Iron Man 3, Tony spends a good deal of time in hiding with many people believing he was dead. Meanwhile, he was tracking down terrorists who had also been hiding so if anyone was coming to look for him, he would be impossible to find. Additionally, War Machine spends much of the time on missions in the Middle East or has his armor stolen, so he couldn't help much, either.
Thor: The Dark World, as the name implies, has Thor traveling to the world of the dark elves, so he is not even on Earth.
From all indications, Captain America: The Winter Soldier has both Captain America and Black Widow on a secret mission against SHIELD double agents, so secrecy is also a top priority, much like in the Iron Man example.
The Incredible Hulk obviously would not be helping out since he spends his time either as a normal scientist or a mindless monster who may cause more harm than good, so it's best for all involved if he lays low.
The Animorphs get the chance to acquire dinosaur morphs when they go back in time; the ending provides a Snap Back so that they cannot use these morphs in the future; random Techno Babble at the end of the book gives us an explanation why.
There's also the Chee, the ageless androids who could obliterate the Yeerk threat with their eyes closed, except for the fact that they're hardwired never to harm anything. Erek does briefly do away with the violence prohibition and he absolutely slaughters a force of Controllers. He kills them all so violently that it reduced Blood Knight Rachel to tears. For bonus points, Erek, being an android, has a perfect memory that never fades or forgets. He's so horrified by what he's done that he rewires the violence prohibition right back in.
In the Harry Potter novels, Albus Dumbledore almost always seems to have a pressing duty that makes him leave Hogwarts just when Harry is about to get stuck fighting some highly dangerous bad guy:
Philosopher's/Sorcerer's Stone: Dumbledore is off at the Ministry of Magic when Quirrell decides to steal the Stone. In this case, the summon he receives from the Ministry is fake, made so he'll be away when Quirrell carries out his plans.
Chamber of Secrets: By the time Harry and Ron discover the entrance to the Chamber, Dumbledore has been suspended by the school governors.
Prisoner of Azkaban: Played with, since it's Dumbledore himself who tells Harry and Hermione what to do, because they were the only ones who could.
Half-Blood Prince: Exception, Dumbledore takes part in the climax and is killed.
Which also works as this trope for the series as a whole, since it was Voldemort's plan to get rid of Dumbledore first, and then try and take over the world.
It is eventually explained in book seven that Harry needed to defeat Voldemort himself in the end, so Dumbledore had to let Harry build up enough skill over the years to do it. Unless he absolutely had to intervene, or if something happened he hadn't planned for, he let Harry do it, giving him just enough skills and information beforehand to let him succeed.
In The Lord of the Rings, Gandalf combines this with standard Deus ex Machina heroics when he leaves Helm's Deep to fend for itself against the Uruk-Hai siege so he can gather troops for a Big Damn Heroes moment. Not really unexpected, given that he also left Thorin's party to check Dol Guldur in the middle of The Hobbit. Part of this is the implicit idea Gandalf is conflicted on how much to affect events, which would make him too much like Saruman.
This happened in the first book too, when a Balrog dragged him into a chasm in Moria.
On a larger scale, Higher Powers have forbidden him and the other wizards from engaging Sauron directly, out of the fear that doing so will destroy still more of the world.
In fact, even the powers the wizards could use are extremely limited due to their physical "human" forms. It's unlikely Gandalf could have turned the tide at Helm's Deep alone, making his flight to gather reinforcements critical.
Unfinished Tales contains The Quest for Erebor, which is essentially Gandalf explaining all the things he was doing while he was absent for parts of The Hobbit, and how important they were.
The Eagles are used as Deus ex Machina on several occasions in Lord of the Rings books to solve a particular problem, but for the purposes of this trope then vanish until next time despite the fact that they could easily bypass most of the trip using them, with even less justification for it given in the movies. This point is repeatedly parodied in several Lord of the Rings HISHEs.
The Call Of Cthulhu sees the briefly awakened eponymous Eldritch Abomination go back to "sleep" instead of destroying the world, in one of the rare villainous versions. There's a good reason for this, made clear in the story itself.
Conan of REH's Conan the Barbarian series has this happen to him in A Witch Shall Be Born. He gets captured by Salome's henchmen, and crucified outside the city gates; an Arabianesque fellow who happens to wander by takes Conan down. Conan joins his little bandit gang and spends a good deal of the story pillaging and doing things outside of the city-state of Khauran where most of the story transpires; leaving the young guard to be the hero of his own story.
Also in Beyond the Black River, where Conan heads off to make sure one group of civilians are safe, leaving Balthus to do the real heroism as he arranges for people to be evacuated and covers their escape with a Heroic Sacrifice, saving many.
In the 7th Haruhi Suzumiya novel, Mikuru gets kidnapped by some hostile organizations. What follows is a carchase with Mori and Arakawa from the organization. Of course, Kyon could have just called Yuki for help, since she's just about omnipotent. This is justified by a) there was not much time and Kyon was in serious panic and b) He doesn't like to rely on Yuki, because he already owes her enough. The best thing is when Kyon actually thinks what would have happened if Yuki was involved. To quote the man himself:
"There's no way four mere kidnappers could beat the formidable Nagato, but I'd certainly look forward to such a scene."
Michael Carpenter in The Dresden Files gets this a lot. In every appearance he makes Michael gets sidelined for some reason or another. He gets his sword stolen by Harry's faerie godmother in his first appearance, gets arrested for several days in Missouri in his second, and gets stuck in Oregon in his third appearance. It doesn't help that the last two occurrences were off-screen. He did get some badass fight scenes in Death Masks and Small Favor to make up for it though. It is also strongly implied that Michael is dramatically more powerful when God himself is giving him the task he's setting his blade to, turning him from a fairly strong hero with a big sword to a righteous force of pure, evil-smiting destruction.
In-universe, the use of this trope is justified in that the knights of the cross are expected to be good or virtuous in all things, so when they're not divinely mandated to be somewhere they're easily distracted by helping a little old lady cross the street, if they stop a mugging they'll also make their court date to stand as an honest witness, and so on. Their militant aspect is implied to be god's measure of last resort, so the call to action (and associated "right place at the right time" power) only activate if evil is otherwise inevitable. So long as Harry and his other allies have things in hand, God isn't going to hot-drop his personal SEAL team into the situation. Narratively, the trope is probably used just because Harry would be much less of a The LonerHurting Hero if his powerful, competent friend were actually reliable.
Averted for once in Small Favor when Michael singlehandedly clears a train station of hundreds of Hobs. Only after Harry has cleared the myrk though, and meanwhile, Harry himself is occupied by fighting one big monster rather than hundreds of small ones.
Happens to Harry himself at least twice.
When Mab takes his blasting rod and relevant memories, in-universe, it's because that kind of magic would attract the kind of monsters he was dealing with. Narratively, it's because he could have taken them apart easily with his usual resources, and she only did it at the point in the story where they didn't matter any more.
When he is dead, Chicago becomes much less safe for ordinary people and his friends.
In Over Sea, Under Stone by Susan Cooper, Ms. Palk tricks Merry to drive somewhere far away because Simon, Jane and Barney went there, while really the kids are being chased by Hastings and his goons.
Aslan in Prince Caspian, who is prevented from stopping the Telmarines from almost wiping out the Narnians, and thousands of years later, doesn't arrive to save them until the last minute, because he can only show up once somebody's faith has been tested.
Aslan also gets this in the earlier The Lion, the Witch, and the Wardrobe, only this time he has a good reason he's dead, having sacrificed himself to save Edmund from the White Witch, leaving the heroes to rally the good army without him, and prove their worth. Aslan, meanwhile, recovers and pulls off an awesomeBig Damn Heroes moment.
Luke does this in the Black Fleet Crisis, first going off to try the life of a hermit in utter isolation with no contact from friends and family - a decided change from his usual involved do-gooder attitude - then going with a woman who claims to know his mother on a long and ultimately completely pointless and irrelevant journey, while his friends struggle with a serious war against genocidal opponents. The author took pains to reallyescalate Luke's abilities in this trilogy, too.
Many books in the Star Wars Expanded Universe give Luke separate Plot Threads which may or not seem related to what the others are doing at first glance, but usually conclude with involvement in the rest of the story. Timothy Zahn does this masterfully, often weaving the threads together and parting them so that whenever Luke's removed from the scene so that the other characters have to make do without him, it never feels contrived.
In the Honor Harrington novel Crown of SlavesGenius Bruiser Anton Zilwicki, experienced spymaster and slayer of Super Soldiers who would probably have soloed both the villains' plot and minions, takes a mission that puts him out-system for most of the book.
In the first book of The Death Gate Cycle, Haplo explicitly notes that if he used his Patryn powers he could solve all of the book's problems in about two minutes...and then the Sartan would blow up the world again.
This is done to various alien races and civilizations in Stargate SG-1 to keep the protagonists from getting too powerful, too fast. Most of them hide behind some sort of Alien Non-Interference Clause, but in some cases it's just because they are exceptionally difficult to contact, or when they are contacted they are "too busy".
The Nox decided to cut themselves off because they think that everyone else is too "young" and that they won't know how to keep from killing themselves and everyone else if given advanced technology. That's fine and all, but they seem to take it to an extreme.
The Tollans are afraid to give away tech after they watched the people of their neighboring planet kill themselves with the stuff they gave them. They do at least make alliance with Earth and help out from time to time, but they still don't offer any knowledge or technology.
The Tok'ra seem to expect more of the Tau'ri than we're permitted to expect of them, despite being among Earth's closest allies. They're more than happy to give the SGC something to do or use SG-1 as their personal test subjects, but try to call them and either the line doesn't get through or you get a busy signal. Then they have the gall to criticize the Tau'ri for acting without them, or doing it the wrong way. Where the hell were you then?
O'Neill often lampshades this, and resents the Tok'ra for never being there when they need help, but repeatedly getting SG-1 to go on stupendously dangerous missions for them.
What Ancient allies we do run into never stick around more than an episode or two, most often thanks to the rest of their kind enforcing their Neglectful Precursor ways and stopping them before they can do anything more than point the good guys in the right direction.
Used as a plot device on Buffy the Vampire Slayer; whenever Giles could easily defeat a lesser big bad, he was promptly knocked unconscious to give Buffy a chance to save the day. This was lampshaded repeatedly, and Giles often refers to his "tendency to get knocked on the head". Anthony Stewart Head's fan club actually sent him a number of helmets to commemorate the Tap on the Head Giles perpetually received; he reportedly used one as a lampshade in his trailer.
Inverted in the Season 3 Episode "The Wish", where the characters are dealing with a Sunnydale that Buffy had never visited, and then they make a call to get her to come there.
Giles does get to off Ben/Glory, though.
Willow, post magical power-up, was also removed this way at least once. Anya points this out at one point, noting that the "trap everyone in the house" spell they're under should be no big deal for a witch of Willow's power, but she's still going cold turkey.
In one episode, Xander is forced to stop a group of zombies from blowing up the school, something that would be a minor annoyance to the more powerful characters—but they are kept busy dealing with the much greater threat of the Hellmouth opening.
Buffy runs away from her friends and mother after having to kill her lover. They manage to hold down the fort, though not nearly as well without Buffy. Some spend an entire summer wishing she was back or actively trying to find her.
In Season Eight, during the first arc, evil witch Amy traps Buffy in a nightmare while she attacks the Scooby Gang's new castle HQ with an army of zombies. They are saved by Willow. However, this was Amy's plan; she is able to capture Willow for her boyfriend Warren, who wanted revenge on Dark Willow almost killing him, and also to lure Buffy into the grasp of the General Ripper hunting her. However, Amy's plan backfires when Buffy is able to use what in the dream Amy trapped her in to defeat Amy.
Several times in season 3, Faith disappeared for an episode so that the presence of a second Slayer didn't make the Threat of the Week too easy to beat. Most notable is "Helpless", where Buffy is robbed of her powers by the Council; there's a brief line at the start saying that Faith is "on one of her unannounced walkabouts", and no more mention is made of her.
Rare Sixth Rangers in Power Rangers who don't suffer depowering courtesy of Good Is Dumb get saddled with this instead, with the exception of the even-rarer Ineffectual Loner Ranger. This is usually the case with team additions who start out evil; once they turn good, excuses are made for them not to be on the field of battle rather than run the risk of suffering Badass Decay. These excuses can go as far as half-season absences while they're off researching enemy motives, to as little as being so constantly late they couldn't hold a proper job if they ever tried to get one.
Udonna from Power Rangers Mystic Force loses her staff that lets her become the White Mystic Ranger for most of the season, but she's still a powerful sorceress. Yet whenever the Rangers have a problem that she should be able to solve in a matter of seconds, she is nowhere to be seen, let alone mentioned. note Probably helps that her Mahou Sentai Magiranger counterpart, Magi Mother, is dead through most of that series
And of course, the original Mighty Morphin' Power Rangers had Tommy and his "swiss cheese brain" that would cause him to forget important things (like his morpher on at least one occasion) and be unavailable to fight the Monster of the Week. This had a Real Life explanation as well, since Tommy's Japanese counterpart pulled a Heroic Sacrifice and wasn't around nearly as much, a problem rectified by Toei producing brand-new suit footage for the second season.
In Tommy's introduction, the "Green With Evil" miniseries, the first thing Rita Repulsa does with her new evil Ranger is get him into the Command Center and cut Zordon off from Earth so he can't intervene. The Rangers are subsequently stuck on the defensive until they can reestablish contact.
This is usually carried over from Super Sentai, whose fans refer to the trope as "Sixth Ranger Syndrome." Prominent examples are Genta/ShinkenGold in Samurai Sentai Shinkenger, who would either be running his sushi stand during important battles or sent off on completely separate missions from the rest of the team; Gai/GokaiSilver in Kaizoku Sentai Gokaiger, who breaks his arm as an excuse to have him stop fighting for several episodes. He also is mostly absent, without much excuse, from The Movie; and Yuusaku/MegaSilver in Denji Sentai Megaranger, deliberately written so that at the start of the show the character could not transform for more than a few minutes at a time due to a fault with his suit (and when he fixes it, the suit loses a lot of its power.); Jin Masato and Beet J. Stag of Tokumei Sentai Go-Busters often will show up later without explanation, after the main three are already in the heat of battle.
An inversion of this occurs in Mahou Sentai Magiranger, where MagiShine sends the rest of the team off on a training exercise while he deals with the Monster of the Week by himself. After that point though, its played straight, with a couple of episodes consists of the main team catching up to him, while he have his own business to deal with elsewhere before he returned in top shape and kicking ass.
The Haitian (whose power is to nullify everyone else's superpowers) is conveniently absent whenever things get really crazy. Heck, the first season finale could have been completely avoided if The Haitian had simply walked up to Sylar and shot him in the head (then again, that probably wouldn't have been according to The Plan).
He finally makes himself useful in the second-to-last episode of Season 3, where he's the key to defeating the Physical GodBig Bad.
Volume 4 revolves around a secret government unit out to capture and imprison every last special. That's a job the Haitian could do overnight if their commander weren't so hell-bent on making it all about us vs. them and probably explains his complete absence during that entire arc.
Likewise Sylar on the villain side. He spent much of the first season locked up and/or catatonic and much of the second season suffering a bad case of being Brought Down to Normal.
The most egregious of these was probably in the third volume when Hiro was given the mind of a 10 year old to prevent him interfering, before the volume's Big Bad completely stripped him of his power.Word of God says that they're trying to write out time-traveling powers from the storyline so they won't have to keep doing this to characters.
Matt Parkman is also a popular victim of this trope after his Psychic Powers start expanding in Volume Three. In fact, in each Grand Finale from Volume Three on, the writers made sure that Parkman was either on the complete other side of the country from the battle or en route and only arriving shortly after the dust had started to settle.
This trope was one of the reasons that the new series of Doctor Who rendered the Doctor the Last of His Kind, so that when things really hit the fan no-one would wonder why the Time Lords didn't decide to use their great smiting powers as they had done on a few occasions in the original series.
The Time Lords return eventually but they are in another Universe and The Time of the Doctor shows them returning would trigger a new Time War. Downplayed when they are able to give the Doctor a new regeneration cycle, which enables him to regenerate and destroy the Daleks.
The Doctor spent the majority of the new series's first Christmas special in a post-regenerative coma, unable to help his friends and the entire mankind as the world faced a sudden alien invasion. He snapped out of it eventually, of course, and promptly handed the aliens' asses to them.
Additionally in the episode "Blink", he is trapped in the past and only has brief appearances.
And in the two part "Human Nature"/"The Family of Blood", he spends all of the first episode and nearly all of the second as a powerless human, without even memories of his days as a Time Lord (sorta). It is later revealed that he did this on purpose, to give the family of aliens chasing him an opportunity to simply walk away safely. When he is forced to turn Time Lord again, he easily dishes out horrible punishments to all of the family.
So easily, in fact, that it happens off-screen. After he is restored and effortlessly blows up their spaceship, the epilogue is narrated by the bad guy, explaining the horrible fates visited upon his family.
And in "Turn Left", he's not around on account of being dead, because it takes place in an alternate Crapsack World where, because Donna never met him, he died during his What the Hell, Hero? moment with the Racnoss.
Inverted in "Midnight". The sidekick is removed from the picture, and as a result the Doctor fails to save the day.
Occasionally happened in the original series when an actor went on vacation.
Let's not forget all the times K-9 was temporarily out of commission during the Tom Baker years. In fact, Baker lampshaded this in a blooper.
During the Fifth Doctor era, this was done to the sonic screwdriver. It was destroyed and he never built another one for the duration of the original series.
Sort of done in Knight Rider in various ways. When you have a nearly-indestructible sentient supercar, sometimes you have to come up with ways of incapacitating it in order to allow for some drama. This usually involved Michael getting himself somewhere KITT couldn't make it (not that that didn't stop him from turbo boosting into a high-story apartment once...), KITT being incapacitated or stolen/hacked by some kind of Applied Phlebotinum, or outright damaged/destroyed by something. This was never permanent, despite the anxiety it caused, and the Big Bads usually seemed to give them plenty of time to repair/recapture KITT unhindered.
The reverse was done a time or two as well, with Michael being unavailable. This was mostly played for laughs by showing KITT trying to cope with a new driver and failing.
Scott Sherwood is missing from the Halloween episode of Remember WENN with no explanation. One fansite speculated that it was because a character as sneaky as him would have seen through the central deception immediately.
On Supernatural, having Castiel around and fully angeled-up is basically the Easy Button. So he gets hit with this a lot.
The first time, he time travels back to when the Winchesters' parents were still alive, and the effort alone nearly kills him.
The second time, he branded an anti-angel sigil on his chest to send a bunch of angelic Mooks to God-knows-where. This had the nasty side effect of sending him to God-knows-where, as well as stripping him of his remaining powers.
The third time, Castiel is busy fighting an offscreen civil war in Heaven and being one of the Big Bad Ensemble of the season.
The fourth time, after he absorbs every soul in Purgatory, he is soon "killed" by the leviathans growing inside of him. He later reappears as a normal human, without any memory of being an angel, and gets his powers back just in time for...
The fifth time, where he absorbs Sam's memory of being in Hell, which drives him crazy and has him committed in a hospital.
The sixth time, he gets stuck in Purgatory with Dean but stays behind when Dean manages to escape. He is saved by Naomi, who makes him her Manchurian Agent and prevents him from helping the Winchesters any more than necessary.
In M*A*S*H, whenever the CO (Henry Blake in early seasons, Sherman Potter in later seasons) was away, Frank would go about creating his own rules, which created drama that couldn't have happened with the CO present.
The Merlin writers didn't even bother trying to justify why Merlin didn't just call the Great Dragon to his aid every time Morgana took over Camelot. Fan Wank tried to fill in some of the gaps (that Arthur believed he'd killed it, that Merlin didn't want to expose his secret) but it still caused some credibility issues.
In the latter half of the series, Merlin became this. It's hard to write a Monster of the Week that the hero can kill without even moving, so the plots were either things that he couldn't solve by just killing the problem or got him out of the way.
A number of Star Trek: The Next Generation episodes had Deanna Troi absent for at least part of the story, because otherwise her telepathic abilities would have brought the episode to a resolution in a matter of a few minutes.
Mythology and Religion
Older Than Feudalism: Done in the Argonautica by Apollonius of Rhodes (3rd century BCE), when the Argonauts accidentally leave Heracles behind in the land of Kios, while he looks for his lost ward/lover, Hylas. Lampshaded in that same work, when Apollonius mentions that had Heracles stayed with the group, all of their challenges would have become trivial.
In the Big Finish Doctor Who drama Vengeance of Morbius the Time Lords are written out due to Morbius using his stellar manipulator to drain their power. However when the Doctor turns off the manipulator the Time Lords are able to perform a Reset Button, preventing Morbius's Empire from existing. [[spoiler:Too bad Morbius pushes the Doctor down a chasm before the Time Lords do this.
Age of Mythology does this during the expansion. The first game's campaign ends with Arkantos being granted the powers of Zeus in order to beat up an avatar of his brother Poseidon. The ending also implies that Arkantos ascended to godhood. In the expansion, Kronos breaks free despite the event of the first game, when the entrances to Tartarus were either sealed (Ioklos, Atlantis) or in the hands of the good guys. The reason why Arkantos, evidently capable of beating up a renegade god all on his own doesn't whup his ass? Athena promoted him to the god of Titan Slaying and the gods aren't allowed to interfere directly with mortal affairs.
Read that again. Arkantos is the god of Titan Slaying, and he isn't allowed to do his job. Face, meet palm.
He doesn't even slay a Titan. He slays a statue.
Psychonauts has the world-famous psionic superspies Sasha and Milla, who get sent away on "official Psychonauts business" just as things start getting really bad at Camp Whispering Rock. It's later revealed that they were lured to a trap by the Big Bad and had their brains removed. Don't worry, they got better.
Zero for the most parts of Mega Man X. Becomes less and less the case as the series goes on, until full playable status in the fourth game.
Especially noticeable in Mega Man X: Command Mission, where you literally lose him for nearly 1/3 of the game right after the very beginning, considering he's easily the most overpowered character in your party at that point in the game.
Ditto X in Mega Man Zero, and of course his absence has allowed all hell to break loose. It makes sense that his body isn't up trying to blow away enemies; what goes unexplained is why in the hell he never talks sense into the Guardians. And in the Drama Tracks, he even does this - but not until the third game is well underway. Much trouble could have been avoided if he did it, though it is not entirely clear if he could - the one time when he does it, they are badly beaten and unconscious/deactivated for maintenance in a place they would normally not set their foot in.
Auron, in Final Fantasy X, could immediately explain to Tidus exactly why he was in Spira and hand any enemies' asses back to them. He probably intentionally exited himself, just to make Tidus grow (both in strength and in character).
In Fire Emblem: Radiant Dawn, there is a major war between the Laguz alliance (several countries populated by people who have animal forms) and Begnion (the most powerful empire on the game), embroiling most of the continent and exposing the Laguz to great risk, yet both the king of beasts and his second-in-line are not there. The army is going to be marching through a lot of rough terrain and they simply can't afford to have their king that far away from his country. If what happened in the Hawk Nation had happened in the Beast Nation, there's no way he could have gotten back there in time.
In Jedi Outcast, Luke Skywalker fights the Big Bad to a draw, then is trapped after taking a sucker punch, delaying his procession to the final battleground for climactic battle, leaving it up to hero Kyle Katarn to fight the bad guy one-on-one.
Likewise, in Jedi Academy, Kyle Katarn misses out on the final battle because he has to stay behind and save More Than Mind Control victim Rosh, leaving it up to newbie hero Jaden Korr to face Tavion.
In the Baldur's Gate series, the main character will sooner or later run into both Drizzt and Elminster, who will, for some reason or other, never be around to stop the villain's latest scheme (Elminster tending to have more globe-shattering better things to do and Drizzt doesn't think of himself as the type to intervene in every single frickin' crisis). You can in fact get Drizzt and his allies to help you in Shadows of Amn in Storming the Castle of Bodhi's guild, and in Throne of Bhaal it's justified with multiple reasons. First, only Bhaalspawn can open the way to the Throne of Bhaal, and since the gods are forbidden from directly intervening in the Bhaalspawn conflict by Ao Himself, Elminster as a 'Chosen of Mystra' would likely be barred from participating. The one time you do encounter Elminster face-to-face, he muses you and your party are probably powerful enough to battle him to a draw at the least, and might even be dangerous enough to kill him. And Drizzt is about on the level of your average cannon-fodder by that point.
In the Touhou series, Reality Warper Yukari Yakumo is just plain lazy. On the few occasions in which she has actually woken up, she hasn't shown anything close to the power she showed as a Bonus Boss. In Imperishable Night and in the fighting games, she's just an ordinary playable character; in Subterranean Animism, she stays home and lets Reimu do all the actual work (because surface youkai aren't allowed underground).
The main thing here is that dealing with incidents is the humans' job (especially Reimu's). That said, she does beat the hell out of Tenshi and stop her plans more or less single-handedly. And of the few really dangerous incidents the only one she didn't help resolve is the one she caused.
In Chrono Trigger, the lead character is blasted into ash by Lavos in the confrontation at the Ocean Palace, very effectively knocking him out of commission. The rest of the party can then undertake a lengthy sidequest to get him back, but it's not mandatory.
Mass Effect 2 has Joker's mini-mission. The Normandy is out of commission for a few hours, and all of its systems are offline, including the huge cannons Shepard just installed and the FTL systems. In short, the Normandy is absolutely helpless. So what does Shepard do? Leave the Normandy for the next mission. And take the entire squad along, leaving the crew to fight for themselves for a while. What Could Possibly Go Wrong??
EDI: "I have detected a signal embedded in the static. We are transmitting the Normandy's location."
Joker: "Transmitting? To who?"
(The Collectors drop out of FTL directly above the Normandy. The Collectors board and begin to capture or kill the Normandy's crew.)
Saber in Fate/stay night is essentially immune to all magic. The plot of most of the second route, UBW, is about dealing with Caster. Well, we can't have our main fight be completely immune to the bad guy's power, can we? So the contract between Shirou and Saber is cut, Caster captures her and tries to make her kill Shirou. However, she conveniently resists long enough for Caster to die to someone else entirely and then suddenly a new contract is made with Tohsaka!
Raiden, dear Lord, in Metal Gear Solid 4: Guns of the Patriots. You see, by that point, Raiden has gone from complete wimp to even stronger than the legendary Gray Fox...and he spends most of the game disabled. It begins with his first fight against Vamp, making him absent for one quarter of the game. Then, he's back... in time to make logic defying decisions that will leave him even more crippled (Raiden: "I'll cover your back" ...WHAT? I'm riding the ultimate machine of destruction. If anything, you need me to cover your back...) and slightly more ridiculous (Don't worry Snake, I'll save you from this giant submarine by making the reversal of what any sane man would do! I will hold back the giant thingie! GO ME!). As a result, Raiden is, by the climax, little more than a tragic version of Monty Python's Black Knight.
Not really, Raiden essentially exists to negate Vamp as Old Snake is in no shape to engage in a hand to hand fight by this point. Stopping the super submarine was questionable though, but it didn't prevent Raiden from helping in the next chapter anyway to make sure Old Snake made it to the control center. The only reason he wasn't there at the very end was that It was a suicide mission and Old Snake was already transforming into a WMD
Conversely, this is done to a point in Metal Gear Solid 2: Sons of Liberty. Solid Snake, still in his prime, is "killed" when the tanker is ripped apart by Revolver Ocelot. This accident is considered an environmental disaster and Snake is vilified. This is the whole reason for the introduction of Raiden in the first place.
Probably the most annoying quest (out of many) in Star Control 3 involves saving the Chmrr after the Daktaklakpak successfully commit genocide against them. The probable reason for including it? To sideline the Chmrr's super-powerful fleet until the war is pretty much already over.
In Star Wars: Knights of the Old Republic I and II, there are several instances where the player loses the use of a strong party member or has to play as someone other than the player character.
Half-Life 2 and its subsequent Episodes has Dog. During his brief periods of time with Gordon, Dog has crushed squads of Combine soldiers, fought a Strider (barehanded and solo) and won, and even manages to severely injure one of the horrifically powerful Combine Advisors. Naturally, events repeatedly conspire to prevent Dog from being with Gordon to prevent this unstoppable engine of destruction from obliterating anything and everything in the player's path.
X-Men: Next Dimension: The Juggernaut lunges at Bastion, who responds by simply using a power ray to teleport him offscreen; in one ending, we see that he was sent to Mars, where his power basically keeps him alive without needing food, water or breathable air, so he could potentially stay there forever, alone.
The post game, Broken Steel Add On for Fallout 3 should be a cakewalk. After all you've got Liberty Prime, the giant robot the Brotherhood spent the entire main game trying to salvage, that turned the tide in the final battle of the main game, on your side. Then he gets crippled by an airstrike in the very first quest and will take YEARS to repair. So yeah, don't count on him for the rest of the add on.
In Armored Core: For Answer, the only major power opposing the League of Corporations, Line Ark, and its greatest military asset White Glint (the player character from AC4), who is so feared by the League that they insist on sending their best LYNX with back up to take him out, are taken out of the picture just in time for the game's real plot to kick in.
The twin goddesses depart for the heavens at the end of Ys II, although they make a reappearance in The Dawn of Ys, which is Canon Discontinuity according to Falcom.
In Injustice: Gods Among Us, Superman is in outer space fighting Doomsday, so he isn't taken to the alternate universe with the others. Although subverted, as the Batman of the Injustice-verse, who brought everyone else over, is understandably skeptical of bringing another Superman over, seeing how his universe's Superman is the Big Bad. The real Supes is only brought over because of the demands of his universe's heroes, The Flash of the real world powering a portal that Cyborg already used, and a healthy dose of crossing the Godzilla Threshold.
In Nine Hours, Nine Persons, Nine Doors The Nonary game's digital roots are the keys to escape. Certain doors on the ship contain numbers painted on them in red paint. These numbered doors can only be opened when the numbers of bracelets verified have a digital root of that number. If the digital root of these numbers is not the number on the door, the RED will read "ERROR" and the screen will clear. The number 9 is an extremely valuable and versatile number, as it is the only number that will not change the digital root of the number it is added to. This means that the bearer of the number 9 bracelet can more easily control his fate than the other players, as he can join any team whose digital root is 9, even teams of two. So the number 9 bracelet is given to a Sacrificial Lamb character in the game's prologue to increase the stakes.
In Pokemon Mystery Dungeon Explorers, Grovyle is one of the three chosen ones permitted to enter the Hidden Land to attempt save the world (The others being your hero and partner). He's usually shown to be more competent then them in cutscenes and is likely to be stronger in gameplay, so naturally, he ends up performing a Heroic Sacrifice just before the final dungeon, forcing the two to get the job done themselves.
In Pokémon Mystery Dungeon: Gates to Infinity, this is presumably why Hydreigon ends up being taken out of the picture by Kyurem. Saving the world would've been much easier had he been able to stick around as he intended to.
DM of the Rings brilliantly parodies Gandalf's tendency to do this in The Lord of the Rings (see Literature). After the entire night of fighting at Helm's Deep Aragorn, Legolas, and Gimli are all talking about how they will now finally get some respect from these people. Three guesses who suddenly shows up at the last minute after all the hardest work is over, and is being praised by everybody else.
Gimli: It was a lot of work, and I'm sure we'll get jack squat for the reward, but at least we'll finally get some respect from these people. All we have to do is finish off the rest of these orcs. (Gandalf shows up suddenly) Everybody: Gandalf has come to deliver us! He's saved us! HAIL GANDALF!!! Aragorn: That guy is really starting to get on my nerves.
Howard Taylor of Schlock Mercenary has mentioned this as a problem for writing when Petey has ascended to a higher state of being but stuck around with virtually omnipotent powers. However, he's introduced a horrifying limitation that cripples Petey: while he could instantly teraport anything or anyone in the galaxy anywhere he wants at will, he needs every watt of energy to save trillions of sentient life-forms in the Andromeda galaxy, and each time he meddles with the main characters represents a sacrifice of lives he could have saved.
Lampshaded in the arc that introduced the limitation:
Petey: "Insufficient resources"? What happened to God Mode?
Andy Weir, writer of Casey and Andy, has referred to the same problem; since Satan is a regular member of the cast, and on the nominally good side, he needs the find some way to indispose her before any arcs can progress.
Dragon Ball Multiverse: The Vargas could have sent every particle of Universe 20 back in an instant if U4 Buu didn't sabotage the machines.
The Whateley Universe has this problem with some of its more powerful protagonists. Some stories have had to find 'reasons' why Tennyo (or the headmistress) couldn't step in. In "Boston Brawl II" they solved the problem by having Tennyo go after the one supervillain she couldn't beat.
Even better, in "Ayla and the Great Shoulder Angel Conspiracy", the authors came up with a way of stopping Tennyo, maybe for good, by confronting her with the past of her alien part and giving her a Heroic BSOD.
In Vaguely Recalling JoJo, DIO and J. Geil had to take Enya to hospital, so the Hanged Man and the World Stands can't take Steely Dan and the Lovers Stand out with ease.
In Noob, the second episode on the Dungeon of Chaos three-parter had Fantöm go after Tabris, which kept him from participating in his team's high-level Boss Battle.
In Worm Scion is practically omnipotent, but he's busy with the minor disasters constantly happening all over the world and noone knows how to contact him to call his attention to the really serious ones.
Justice League and Justice League Unlimited loved this trope so they could focus on specific characters. Fights would have been boring with the Martian Manhunter (the King of Combo Platter Powers) and Superman kicking the ass of everything that came to Earth, not that they didn't get their share.
And, of course, there was "The Greatest Story Never Told", an episode focusing on perpetual Butt MonkeyBooster Gold, who had to deal with an alternative power source gone berzerk while the entire rest of the League battled a godlike foe. Naturally, none of them believed it had ever happened. Of course, he did get a hot scientist chick to compensate and didn't have to help clean up either his mess or the mess the League caused, so it worked out pretty well.
Subverted in "In Darkest Night, Part I", which very conspicuously pointed out that Supes was busy with an earthquake in India...only to have him show up halfway through the episode anyway. He mentions that he finished early because the earthquake was "only" a 4 on the Richter Scale.
And in the episode "Patriot Act," the entire rest of the League is busy, so the five non-powered heroes who were available are sent to walk in a parade in Metropolis, later to be joined by two (also non-powered) reservists to deal with the newly superhuman General Eiling. They get absolutely thrashed, but did it in a pretty awesome way, especially with Shining Knight's Shut Up, Hannibal!Crowning Moment Of Awesome in which he talks down the overly patriotic Eiling with his own American ideals—despite the fact that SK himself is a medieval European.
In the episode "Chaos at the Earth's Core", the miniature red sun of Skartaris weakens Supergirl's powers almost to nothing.
In the film Justice League: The New Frontier, Superman is struck down by the big alien monster and everyone thinks he's dead — so that the rest of the Justice Leaguers and the U.S. government have to put aside their differences to beat the thing without him. Aquaman shows up to bring Big Blue back home once the threat is gone.
In the series finale of Avatar: The Last Airbender , Iroh refuses to fight Fire Lord Ozai because — even assuming he won — it would not bring true peace, being ultimately nothing more than "a brother killing a brother for power." This leaves it up to our plucky hero Aang to face the Fire Lord himself.
In "The Desert" episode, Katara has to lead the group because Aang's too upset over Appa, Sokka is high, and Toph can't see (she's blind and senses vibrations) because of the loose sand they're walking on.
Appa himself: he lives and breathes this trope for the entire series. For the record, Appa is a ten-ton (that's twenty-thousand pound) six-legged flying bison with horns. Yet he's only in three battles throughout the whole series and only attacks people in one of them. Case in point: in "Jet" he is literally five yards behind the group as they're walking through a forest, but as soon as they stumble into a Fire Nation camp and get attacked, he's nowhere to be seen. The writers don't even give him an excuse, he's just gone.
In the second season finale, Aang unlocks his chakras, allowing him to enter and exit the Avatar State at will. During his next transformation, Azula sucker-punches him with lightning, closing his last chakra and preventing him from entering the Avatar State. While fighting Ozai in the series finale, a strike in just the right place unblocks that chakra, and Aang finishes the fight quickly.
In the Season 3 finale of ReBoot, the home world of the main characters is being destroyed by Megabyte, who is attempting to escape the dying system. In an effort to save his friends and family, as well as countless others, Enzo squares off against Megabyte with nothing but his girlfriend's trident (he threw aside his gun). Sounds great and suspenseful...until you realize that Bob, the Guardian-Keytool Combo Hero is chilling with Hexadecimal in her lair (okay, not so much chilling, as her prisoner). He manages to get back just in time to miss Megabyte's defeat. It's even punctuated by the standard "What'd I miss?"
In W.I.T.C.H., once Queen Elyon realizes her true powers and comes to the side of good, she should be able to make fights a lot easier, right? After all, she can warp reality and is probably more powerful than the five Guardians put together. However, during the first part of the second season, she's stuck taking care of the daily affairs of Meridian, and during the second half of the season, she's tricked into giving up her power and stuck inside the Seal of Nerissa.
When the 90's X-Men cartoon adapted The Phoenix Saga, the writers had to get rid of Rogue for the first episode (Xavier mentioned that she was away on a mission), since her Power Copying and Flying Brick powers would have solved the atmospheric-reentry problem far too easily. This is lampshaded when she returns, where the first thing she says is that she should have been there since she could have handled it. In the comics, she didn't exist as a character yet, and so she wasn't around to absorb the rescued astronaut's piloting skills and calmly bring down the shuttle as the solar radiation harmlessly bounced off her invulnerable body, with the astronauts and other X-Men safely in the shielded area. No fuss, no muss, no unstable cosmic entity.
Wolverine was subject to this in two occasions in the series ("Reunion (Part 2)", and "The Dark Phoenix Saga (Part 1): Dazzled"). In both cases, the X-Men were defeated in battle and imprisoned and had their powers nullified in some way (the nature of the savage lands in the former and through special handcuffs in the latter). For Wolverine, this would make the inevitable breakout easy due to his adamantium claws since even in today's comics his claws are unaffected by power nullifiers and could cut through anything including the prison bars for the former and the handcuffs in the latter. Hence why at the beginning of each fight Wolverine would be taken out quite early (thrown off a waterfall in "Reunion (Part 2)" and smashed 5 floors into a sewer by Harry Leland in "The Dark Phoenix Saga (Part 1): Dazzled".) Arguably, this helped his character as it gave him a Big Damn Heroes moment.
Another Wolverine example comes from Scott and Jean's wedding (the first one). Wolverine is busy slicing up holographic enemies (some that bear striking resemblance to "Slim" Summers) in his tux during the nuptials. The poor hairy, Canadian shmuck can't stand seeing the object of his affection married off to Cyke. Had he chosen to attend, he would've revealed the big shocker that not only was Morph alive, he was impersonating the Priest as part of a plan to destroy his former comrades.
Often happens to Jake in Adventure Time, usually without any explanation beyond his laziness (when they even explain it that much; often he's simply absent). For example, in "It Came From the Nightosphere," Jake is nowhere to be seen. That is, until the end, when it is revealed that he was shrunken down and residing inside a pocket of Finn's shirt the whole time for some reason.
In Ben 10: Alien Force Alien X is basically a god. They write him out by making him unable to use his powers without a quorum from Ben and two very opposed personalities.
On Beast Wars, Optimus Primal's transformation into Optimal Optimus made him larger and more powerful but for the most part, it just made him a bigger target for any Predacon knockout dart that would take him out before he could curb-stomp the Predacons. Rarely did he make an appearance after his initial debut that didn't have him getting blasted or brainwashed, forcing the Maximals to deal with the threat on their own.
Tigerhawk, who is introduced with Earth-shattering (literally) power in the 3rd season, then a few episodes later, Megatron, in control of the Nemesis ship, promptly annihilates him before the series finale.
Young Justice: periodically the Justice League are left indisposed so there's a reason the titular team have to be taking on the biggest issues. In the first season finale the Justice League were the threat because they were being mind-controlled. Partway into the second season most of the league's strongest members are forced off-world to take responsibility for action they were made to do during said period.
Within the main cast, you'll rarely see the entire team together, especially in the second season. A lot of it has to to with budgetary issues, so you'll often have at least several members of the team absent in each episode.
It quickly becomes clear that The Light are constantly invoking this as a regular strategy. Many of the threats the Team deals with are the more profitable operations for the Light, while the Justice League is off fighting a much larger and much flashier distraction.
My Little Pony: Friendship Is Magic has Princess Celestia and Princess Luna. Both of them are the rulers of Equestria and close personal friends of the protagonists, and are capable of truly incredible displays of power, such as raising the sun and moon. The full extent of their power isn't clear, but they're obviously the most powerful good guys in the setting. Yet whenever a serious threat rears its head, they're never as helpful as you'd think they'd be and usually just point the heroes at the problem. Celestia is usually given an excuse for this, but Luna is rarely acknowledged at all. Though that can be blamed on a whole other problem, and the show got better at addressing her as it progressed.
The main plots in the show Wolverine and the X-men relied almost entirely on covert operations and intelligence gathering, and having the wool pulled over the X-Men's eyes more than once. So Jean Grey and Professor X were put into comas(to remove their reducing these plot elements to mere annoyances for the team) and replaced by Emma Frost(who is weaker than Jean and Charles in powerset and skill, not as trust worthy so the others would be hesitant to come to her about their problems and who was responsible for putting Jean and the professor in their comas to aid her plot with the Inner Circle.