"God does not play dice with the universe; He plays an ineffable game of His own devising, which might be compared, from the perspective of any of the other players,note i.e., everybody to being involved in an obscure and complex version of poker in a pitch-dark room, with blank cards, for infinite stakes, with a Dealer who won't tell you the rules, and who smiles all the time."
CLAMP has been guilty of this in several series, thanks to Clow Reed, his reincarnation Eriol, and his old partner-in-crime, Yuuko. In Cardcaptor Sakura Clow and Eriol frequently manipulated the cast, threatened Sakura's friends and family, and even risked erasing everyone's feelings of love, and yet are still considered good because it was "necessary" for Sakura to be subjected to these things. (Sakura didn't even want to be a mage at first, and in the anime it's not necessarily clear what the pressing reason was for her to become one. Clow's even responsible for the cards escaping when they did. In the manga, it's made clearer: if he didn't do what he did, the magic of the Clow Cards would fade, and two of her friends would die.)
Also, at the end of both arcs, Sakura and the readers find out that there was no "disaster" (everyone losing their feelings of love), and that Eriol made sure that nobody not already involved with the Cards was anywhere near his magical disturbances. Sakura forgives them when she finds out, and even says she's glad she didn't know that there wasn't any real danger, because she wouldn't have tried her hardest.
Sailor Pluto from Sailor Moon, particularly in fanon. Fanon also tends to have Pluto called on this, frequently in the form of losing her powers (oh, the irony).
There's an entire manga about this trope, a shoujo/josei series named Seigi No Mikata (Ally of Justice). The protagonist's sister is a loud, lazy, gluttonous, extremely manipulative cow, but somehow all the selfish, self-centered things she does work out great for her and everyone else. Apart form the protagonist, everyone in the series adores her. Villain Sue, much?
Debatable in Gundam Seed Destiny, where protagonist Shinn Asuka and Older and Wiser hero Kira Yamato ended up on opposite sides of the conflict, which obviously lead to trouble and flame wars (which still continue years after the series' conclusion). Some fans claim the director insisted in interviews that Shinn was always the hero, and that Kira had "strayed from the path of justice", other fans of Kira and his allies insist that they were in the right and that Shinn was the "true villain". (That Shinn spends the climactic battle sidelined after being defeated and humbled by Kira's best friend Athrun, and had up to that point been fighting for the side that Kira and company were trying to stop from using a Wave Motion Gun, probably had a lot to do with that perception.)
The flame wars have gotten so bad amongst Gundam fans, that even after all these years that Word Of God has changed his initial position, and now posits that Athrun was the main character. It hasn't helped.
He hid the Hogyoku within Rukia, causing her to lose her powers and prompting the Soul Society to mark her for incarceration on the grounds of abandoning her post. It was Aizen who ordered her execution under the guise of transferring her powers to a human, but either way, Ichigo decides to swoop in to save her. He's Easily Forgiven by Ichigo after apologizing for it.
He prompts Orihime to train with Rukia, which allows Ulquiorra to ambush her while traveling from the Soul Society to the real world. He forces her to leave with him for Hueco Mundo, and it quickly leads to her friends attempting to rescue her. It forced Yamamoto to send a rescue party for the rescue party, which halves the strength of the Gotei 13 and allows Aizen to enter the real world. The only reason it didn't fail utterly was because Urahara developed a countermeasure for the last part.
In his training with Ichigo, the Shattered Shaft fully gave birth to Ichigo's Superpowered Evil Side. It indirectly saved his life versus three times over, but it develops into an Enemy Within situation that had to be tackled by the Visoreds (whom Urahara did not contact, mind you).
In the Suzumiya Haruhi series, Present Mikuru will accept any indignity, abuse or manipulation that her time-traveling superiors throw at her, because, you know, the future will get messed up if she doesn't. This is averted in the later books, when Kyon calls them on this, explicitly stating that he believes them to be manipulating Mikuru for their own selfish goals, and not for the good of the timeline. This is made even more tied to the timeline (creating a Stable Time Loop) because Present Mikuru's boss is her future self.
Averted in Dragon Ball Z: after Trunks' first time travel and after he has warned the heroes about the incoming threat of the Androids, Bulma suggests seeking out Dr. Gero, the Androids' creator, and kill him before he can enact his plan, which they know for sure he will enact. Goku refuses, partly because he wants to fight the Androids, and partly because he doesn't think it's right to kill someone who still hasn't done anything bad (forgetting that Gero was the lead scientist of the Red Ribbon Army, and so most of their tech was probably built by him).
Aeolia Schenberg from Gundam 00 is revealed to be one of these when its revealed that his plan was that if mankind did not change than he would force them to change using Celestial Being. While his plan is hijacked a couple of times it's put back on track by the heroes.
In Goshuushou Sama Ninomiya Kun, the hero and heroine's family is a mass of absolute jerks willing to continuously mentally and physically torment the main characters, up to and including faking their own death just to get them riled up, as part of a "training" course. While they aren't explicitly stated to have God-like powers, their ability to be anywhere and everywhere at once borders on Deus ex Machina.
After being revived, Itachi pretty much gets his revoked and admits that in the end his attempts to fix everything himself failed and just created a giant mess. He warns Naruto not to make the same mistake.
There is also The Fourth Hokage, Minato Namikaze, who decided to seal the Nine Tailed Demon Fox into Naruto, simply with the conviction that it was his responsibility as a parent to have faith in his recently born son's ability to set things right as motivation. Contrary to the above example, this gambit is turning out surprisingly well, irresponsible though it was.
Minato had another, better reason to do what he did. If Kushina sacrificed the last few minutes of her life to temporarily kill the Kyuubi with her, the Kyuubi would have been resurrected at an unspecified time and place. Given who they were up against and the power of the Kyuubi (and his ability to control the Kyuubi), sealing it in Naruto at the cost of his life may have been the only guaranteed way to prevent another, more successful attack on Konoha.
All of the ruling Elites in Ai No Kusabi for keeping slaves and how they treat everyone in castes beneath them. It's their right as the Powers That Be to do as they please with those below them within their society. Iason Mink really takes the cake however as the most powerful Elite with his treatment of his Sex Slave Riki.
Charles, Schneizel and Lelouch from Code Geass seem to believe they have this. Both them have the belief that what they're doing is completely justified and will turn out well. What they're doing is, in order, a) killing and enslaving entire nations for the sake of a "world free of lies", b) destroy civilization so that he can stop war by using threat of force, and c) make everyone suffer so much that when they stop suffering, everyone will be happy and peaceful for an indefinite period of time that seems to be suggested as "forever". Charles and Schneizel suffer Lelouch's wrath for their actions. Lelouch, as the protagonist, succeeds through methods that are not explained to us, within 3 months of real time, during a time-skip, lasting for a period of time that's not explained to us. Lelouch's actions are treated as a good thing, but it's far too easy to draw parallels between Lelouch's actions and Charles' and Schneizel's actions, especially after 2 seasons of self-centered egomania on Lelouch's part.
Tony Stark, in Marvel comics. "I'm a futurist!" Ironically, he's now lost his position, became a wanted man, and had his world fall down around his ears. Bet you didn't see that one coming, eh Tony?
Reed Richards of the Fantastic Four is also an example. He saved the life of Galactus, the devourer of worlds. When a group of aliens put him on trial for crimes against the universe, it's handwaved that Galactus is somehow necessary to the survival of the universe (it later turns out that Galactus is the can for a Sealed Evil in a Can named Abraxas). How, or even whether, Reed knew this when he saved Galactus is debatable, though it should be mentioned that what brings the decision in favor of Galactus is the embodiment of the Universe itself showing up to testify in Galactus' favor.
He could have been extrapolating from nature. Remove a predator from an environment and often the environment will become overrun with its prey. Its still hard to justify since Galactus and his victims are often sapient and free-willed.
Reed Richard exemplifies the trope again during the Marvel Civil War with a sort of Marvel universe variant on the central concept of Isaac Asimov's Foundation series', the fictional mathematical science of psychohistory (wherein one can, with enough time and mathematical expertise, predict the generalized "future history" of mankind through mathematical formulae.
Using his new mathematical science, Reed Richards discovers that if the new Superhuman Registration Act, which would require all superhumans to register their identities with the government regardless if they rely on the identities' secrecy for their own or loved ones' safety, doesn't pass and come into law the resulting fallout would lead to the deaths of "billions". This discovery is what prompts Reed's decision to support the act.
In another comic example, an early Golden Age superhero known as Stardust the Super Wizard is virtually all-powerful and, from the readers' perspective, quite insane. Yet he always winds up being treated as a hero in the story.
Cable generally acts like this, thanks to coming from the future and already knowing how everything turns out.
Curiously, although he's also from the future and is accompanied by a floating repository of 21st century history, Booster Gold doesn't.
Lucien Draay in the Knights of the Old Republic comics thinks he has one of these, and acts accordingly (to be fair to Lucien, his mother and closest friends are all absurdly powerful seers, so he has reason to believe this). Unfortunately, he interpreted everything they said through the lens of his Treacherous Advisor, who was really a Sith Acolyte working to bring it down from within and used Lucien as a convenient pawn to accomplish this. Lucien's response to learning he's been had could basically be described as: Villainous Breakdown, Villainous BSOD, Heel Face Turn.
Marvel's Odin pulls this a lot. He repeatedly screws with Thor in every way he can come up with, usually as a pretense to teaching Thor some greater lesson. The entire reason Thor is on Earth in the first place is because Odin thought it would build character. Probably his worst offense is the massacre of an entire sentient species to create the creature Mangog. His only defense is the fact that he is Odin the All-Father, creator of humanity, and therefore answers to no one. (Except for when he does, because Thor comics suffer the same continuity problems as everything else)
In respect for Mangog' the race in question invaded Asgard after brutally conquering numerous galaxies. Odin's actions were in defense of his realm and punishment of a a vile race. Odin eventually restored the race to life after the entire species reformed.
In some cases Odin knows of some prophecy or another foretelling great destruction, and is working towards preventing or at least circumventing it by bringing about a Prophecy Twist of his own design.
Subverted to the point of deconstruction in an issue of Impact Comics' Jaguar. The mute, monstrous-looking and -acting antagonist turns out to be an alien that, in an obvious shout out to Superman's origin, was adopted by a friendly Earth couple as a baby, developed superpowers as he matured, was taught to use them for 'good'...and one day started to kill people who hadn't actually done anything wrong. The theory his helpless foster parents eventually pieced together is that his species experiences time nonlinearly, seeing past, present, and future all at once, so he kills people for horrible crimes they haven't committed yet — thereby of course making it kind of hard to demonstrate what they would one day have done to deserve death had they gotten the chance...
The god-emperor of mankind, in his Thousand Shinji role, persuades the other canon!40k gods to send back a sadistic Keeper of Secrets rather than a Lord of Change on the basis that Shinji had to learn that "when the gods are assholes, mortals suffer". Somewhat understandably, Shinji gets enraged and punches him.
The Fans in With Strings Attached. Even though she loves the four, Shag thinks nothing of dropping them into a dangerous environment, completely unprepared and ignorant of everything. Jeft is one of the Big Bads and turns on his own character at the end. And Varx... oh, shut up, Varx.
Drop Dead Fred. The title character does random, chaotic, highly disruptive, and seemingly pointless things, but said actions unfailingly serve to benefit *someone* in the end. One of the best examples was when Fred sinks the protagonist's friend's houseboat. The owner of the houseboat later received a massive insurance payout, far larger than what she expected, and was able to buy a much nicer house as a result.
Although not explicitly stated in Star Wars, Obi-Wan and Yoda used Luke From a Certain Point of View as what they felt was the best way to get him to stop Vader and the Emperor. In the end it's subverted, as Luke wins by NOT heeding their advice. If he had killed Vader like they asked, the Emperor would have won.
Mary Poppins. Those nannies waiting in line in the beginning did not deserve to get blown away in a windstorm, no matter how stuffy they were. Her presence also seems to spread a magical flying hysteria that kills the Bank President, but hey, he "was his happiest in years."
Invoked via the Job argument in "Wholly Moses": "Who are you to question God?" "I am Man."
After a certain point, the entire plot of Paycheck is the main character, Michael Jennings, doing this to himself. He was hired to build a future-viewing machine, with the contract stipulating that his memories would be wiped afterward so he couldn't reveal how it worked. When he goes to collect his payment, he finds that he waived it before the memory wipe. Instead, he is given a large envelope full of seemingly random objects. It is eventually revealed that when testing the machine, he saw a horrific future, possibly caused by the existence of the machine. So, using the machine, he worked out a collection of objects to leave for himself that would result in him blundering his way through saving the world. He worked it out so that he would get a happy ending, but of course he no longer knows this when the time comes and he finds himself facing seemingly imminent and completely unavoidable death.
A lot of people complain how, in The Wizard of Oz, Glinda the Good Witch of the North basically manipulated Dorothy by not telling her how her Ruby Slippers she got when she first arrived in Oz could send her home. In the original novel, this is because it wasn't Glinda (who's the witch of the South) Dorothy met in the beginning, but the other Good Witch, who didn't know how the shoes worked. Presumably, the movie didn't want to use more actors than it had to. The 1978 adaption The Wiz corrects this by having an older witch meet Dorothy.
Subverted in Man on Fire. "Do you think God'll forgive us for what we've done?" "No."
Which is an interesting take on the concept. If he's already irredeemable, there's no reason to have any moral compunction left.
"Forgiveness is between them and God. It's my job to arrange the meeting."
Hari Seldon in Isaac Asimov's Foundation develops a new science - "psychohistory" - that allows him to predict large-scale future trends and future historical events. He further develops a complex plan for the future to create a new Empire. He's the only one that actually knows exactly what it is, but he has a whole planet dedicated to successfully carrying out his 1000-year "Seldon Plan". However, he's repeatedly told everyone that the reason that he can't make the details of the plan itself public is that doing so would guarantee its failure. Someone would eventually use that knowledge to Screw Destiny and cause the plan to Go Horribly Wrong: the predictions made by psychohistory are still vulnerable to a Butterfly of Doom, and psychohistory itself is a powerful enough butterfly to derail any prediction it can make. In fact, the entire plan itself was an attempt to Screw Destiny and create a better future by setting up a planet to become such a butterfly.
And without that licence, he really is kind of a dick. He talks to someone knowing they'll both be arrested for it, because that's part of his plan. He then gets 100.000 of his employees exiled, because that way they are sent where he wants them to go. And that's in the first chapter.
This is ignoring two entire books of characterization. Prelude to Foundation and Forward the Foundation establishes very strongly that Hari was actually a very sensitive and compassionate guy, adopting an underprivileged child, falling in love and being very sensitive to what his new science might mean for humanity. Who it might really apply to is R. Daneel Olivaw, who not only proceeded after Giskard's plan of allowing Earth to die slowly so they would move out into space but also manipulated humanity, albeit subtly, for eons through his various vizier personae, and was instrumental in creating not only psychohistory but Gaia, then summons Golan Trevize to him.
At the very start of Seldon's story, it's established psychohistory can only be used to influence the future in ways requiring such a license - specifically, the concept of a Self-Fulfilling Prophecy is anathema to it. You can't use it to make guesses or estimate the probability or an event. Either the predicted change is inevitable (meaning you've removed any way it could be resisted, including the possibility of other predictors) or psychohistory has nothing at all to say on the subject. At the time Seldon considered this a fatal flaw rendering it useless as a scientific discipline. He was later encouraged to refine it into its completed form as a tool for applying coercive force to shape a society. Why he never managed to expand his work to go beyond the equivalent of "to get a lot of people to exit a building at the same time, set it on fire" is left unclear in-universe; most likely it's Rule of Drama.
Most of the characters' issues with god emperor Leto II in God Emperor of Dune revolves around his near-omniscience and the resulting path he leads humanity down because of it. Duncan Idaho in particular takes issue with it, as well as Leto's transformation into a nigh-immortal sandworm/human hybrid. When queried, Leto argues that the higher morality conferred by his gift of prescience compels him to act in ways that seem unimaginably cruel when the alternative is the complete extinction of humanity.
To be specific, Leto II foresaw that if humanity continued to operate within the confines of the planets reasonably close to Arrakis, as they had been due to the planet's nature as the only source of the spice Melange, which facilitated space travel, that humanity would eventually come to an end. To counter this he ruled over humanity in a reign spanning thousands of years, restricting both their freedom and travel so that as soon as he died humanity would satisfy a three and a half millenia long thirst for freedom and travel and explode out beyond the reach of known space. Humanity would thus be spread out so far and have no vital center, and would thus never end. And It Worked.
Dumbledore's relationship with Harry Potter in the later books begins to resemble this. In the final book, the characters openly question if Dumbledore knew what he was doing. He did, and even correctly predicted that Harry would be willing to sacrifice himself for the greater good. He even knew, or at least guessed, that Harry could survive as long as it was Voldemort that delivered the Killing Curse, but by letting Harry think he would die, enabled Harry to grant his friends the same protection his mother had given him by her sacrifice. He also sincerely loved Harry, and honestly regretted the hell the poor kid would have to go through.
Annalina Aldurren from the Sword of Truth series often invokes this trope, believing that she has a right to steer the protagonist's life because she's spent hers studying prophecies about him. She is quite often called out on this by the other characters (most notably said protagonist's wife), is more often than not wrong in her interpretations of the prophecies, and on several occasions suggests doing things such as erasing the protagonist's memory and having another character seduce him in order to have him do what she thinks he should. In fact, it's outright stated that, had she not meddled in the protagonist's life in the first place, many of the events of the series would never have taken place. Interestingly, Anna is called on this and finally broken of the habit, only for the villains to mess with the timeline/people's memories and her to revert to form.
In the same series, Nathan Rahl occasionally delves into this territory, but is more successful as he's an actual prophet, and gets the total experience and meaning of his prophecies. A more or less straight example: When he's introduced, it's mentioned that while entertaining a young woman, something he whispers to her makes her run screaming from his room, and eventually leads to riots and tens of thousands dead. Much later, he remarks that in that war, a young child died who otherwise would have grown into a horrible dictator who would have killed far, far more.
The Arisians of E. E. “Doc” Smith's Lensman universe use this extensively over a period of two billion years, gradually shaping the evolution of intelligent species and specific bloodlines within those species until their descendant civilizations can defeat their ancient and truly foul enemy, Eddore. They manage all this without ever letting on that they are, in fact, Sufficiently Advanced Aliens to do virtually everything their descendant cultures do, and easily.
Xanth's Good Magician Humfry will send the story's protagonists to face life - and occasionally world - threatening peril with nothing more than an objective and a general path to follow. Justified (albeit by Humfry himself) in that if he gives his supplicants the full story, they'd get things wrong and go straight for the end goal, instead of going through the experience and ally gaining journey actually needed to succeed. (That, and most Xanthians expect to be given the runaround, trusting that things will work out in the end)
Polgara from the Belgariad/Malloreon universe demonstrates this tendency a lot. Admittedly, it goes with the job - Belgarath describes how he often has acted as Aldur's holy hatchet man - but Polgara has the biggest attitude about it.
In Romance of the Three Kingdoms, Liu Bei and his companions (most notably Guan Yu and Zhuge Liang) can do no wrong, even when this means killing hundreds of thousands in various ways over the decades in the name of Liu Bei's vision of supporting the crumbling Han Dynasty, while Cao Cao is the big-time villain despite all the good works, major successes (against others who are not Liu Bei) and personal niceties that he's acknowledged to have.
In book 9 of the Lone Wolf series, the Crocaryx were created by Kai solely to guard a Lorestone. Once that Lorestone is no longer in their possession, the narration announces that this is the beginning of their race's demise. Makes one wonder when humans will fulfill their reason for existing.
In one of the non-interactive novels, Banedon is specifically told that the gods will lend him their aid as long as he's useful to them. Once he isn't, he's on his own.
In S. M. Stirling's and David Drake's series The General, an ancient computer called center (always lower-case) establishes a telepathic link with General Raj Whitehall and drafts him into reuniting the human colony-world of Bellevue in order to restore the lost high-tech civilization of the long-collapsed interstellar Federation. Whitehall is a volunteer in this enterprise and retains his free will — except that center is for all intents and purposes omniscient, and can always show him vividly, with a stated degree of probability, exactly what outcome will result from a given choice, so that Whitehall really has only one way to go.
In Larry Niven's Protector, the Pak Protector Phssthpok feeds the Tree-of-Life fruit to human Jack Brennan, causing Brennan to metamorphose into a superintelligent Protector himself, and then immediately starts laying down instructions about what Brennan has to do to save the human race from a Pak invasion. At one point, as Brennan recounts it later, he is about to protest, "Don't I have any choice?" And then, before he can even get the words out, immediately realizes, "No, I don't have any choice. I'm too intelligent."
In The Wheel of Time, the Aes Sedai all act like this, to the extreme annoyance of both characters and readers. To be fair, some of them are smart enough that things do kind of work out. Others, not so much.
In Dragonlance, Fizban's way of helping people is by being a nuisance and hindering the progress of the heroes, even when it endangers their lives. It turns out his hindrances end up helping them in the end, and that is his unique way of helping them out. He can do this because his secret identity is none other than Paladine, the chief god of light.
The Culture novels are primarily about Contact exercising the Omniscient Morality License they believe themselves to have over all less advanced civilizations.
Matthew Sobol in Daemon or at least his posthumous actions through the Daemon itself.
The Companions in the Heralds of Valdemar series have a tendency to succumb to this temptation from time to time, which is a major reason for their Obstructive Code of Conduct not to interfere with human affairs unless asked. A particular example occurs in the Mage Winds trilogy, when Elspeth's companion Gwena manipulates her toward her Glorious Destiny in an Anviliciously unsubtle way, and is soundly called on it by her Herald. This doesn't stop her from trying, though, and it isn't until Gwena gets a stern talking to from Yfandes in Winds of Fury that she finally gives up.
In Mage Storms, the Gods themselves are revealed to have been playing this game for millennia; nearly every single one of the myriad disasters and near-disasters that have occurred since the first Cataclysm was engineered for the specific purpose of putting in place all the pieces necessary to avert the second Cataclysm.
Dragaera: Vlad Taltos is often subjected to this excuse from his patron goddess, Verra, but he objects rather vehemently to it. After one of her plans blows up spectacularly, he comments to a friend (with whom he had been discussing the concept of the Omniscient Morality License earlier) that he has concluded "when a god does a terrible thing, it's still a terrible thing".
Callum of Raised by Wolves has one thanks to his precognitive powers, and he uses it to justify putting the heroine through an absolutely hellish couple of months, including her being beaten to within an inch of her life by an angry werewolf. In fairness to him, nearly everyone involved does come out of it having lost nothing and gained something. The only casualties are Ali and Casey's marriage and the Big Bad, who deserved it.
The Silmarillion: Subverted with the Valar. Eru gave them almost absolute authority (their authority over Elves and Men, particularly the latter, is a bit of a grey area) over the world, but they lack the "omniscient" part. The Valar can and do make mistakes in pursuit of a greater good, despite (and sometimes because) of their good intentions. The narrative implies that many of their actions (such as bringing the Elves to Aman, or giving Númenor and extended life to the Edain) were entirely the wrong thing to do, even if they were motivated by the best intentions. Some of their other actions (such as releasing Melkor, or sending the Istari to Middle Earth) also had bad results due to lack of foresight (or an inability to understand how good things can become evil). Arguably played straight with Eru himself for giving the Valar authority over Eä even while withholding certain information from them.
There is also the implication that Eru WANTED these mistakes to be made because the whole point of the world he made was to inspire the next great song and conflict somehow just makes things more interesting (never mind that its also bloody miserable)
Subverted in The Wise Man's Fear. The Ctaeh, a faerie oracle, is the ultimate evil. It uses its omniscience to guide whoever converses with it to their doom (and normally to cause massive chaos in the outside world). An entire faction of Sidhe exist just to keep everyone away.
It's revealed in the sixth book of the Emberverse that The Powers That Be are the ones who knocked humanity back to the bronze age, killing billions, because they had foreseen a bad future leading to the extinction of humanity.
Live Action TV
Q, primarily from Star Trek: The Next Generation. He tests the Enterprise crew in various ways, which at times even appear life threatening, but in retrospect it is reasonably obvious that his goal is to assist in the characters' development; albeit in a Zen Survivor kind of way.
Beautifully subverted in the Star Trek: The Next Generation episode "True Q", in which the nigh-omnipotent Q, in one of his rare straight-faced moments, tries to claim this license as the Continuum's right to judge and possibly execute the half-Q, half-human Amanda for being too potentially dangerous to live. When he responds to Picard's questioning that right with the simple, terse words "superior morality", Picard nearly chokes: "superior morality? I haven't seen any evidence of any morality at all!".
Another example occurs in Deep Space 9 with the revelation that the Prophets engineered the birth of Benjamin Sisko. To do this, one of them took control of a woman named Sarah and forced her to romance, marry, and have a child with Joseph Sisko; she left as soon as her body was returned to her. Which sounds a lot like rape, but that implication is never brought up. The heartache it caused Joseph Sisko is, as he thought there was a legitimate romance going on and had no idea why Sarah left so abruptly.
Toward the end of the classic series of Doctor Who, during the epoch known to fans as "The Cartmel Masterplan", the Doctor could often be found pushing the bounds of morality, justified by the incredibly complex machinations of his long-term plans, and the desire of the production team to inject a new sense of mystery into the character.
The Tenth Doctor has shown tendencies towards this too, subverted in that the show treats it as a character flaw, and a very serious one at that. Of course, Ten also gets incredibly worked up over perceived injustices and forms strong emotional attachments to characters he's only known for a few hours, in contrast to classic doctors who held a much more detached attitude. The Doctor's OML finally expired in The Waters Of Mars, where he tried to interfere with a fixed point in time and save a woman who, for the sake of humanity's future development, absolutely must die. She gave him a deeply angry What the Hell, Hero? speech and then kills herself, just to right the timeline.
The 11th Doctor still has moments of this, he is almost as manipulative and secretive as Seven when it comes to using his companions as chess pieces. Seems that the whole "Time Lord Victorious" is still there, he's just a bit more selective and sneaky about how he uses it.
In Power Rangers Mystic Force, senior Knight Daggeron sends the young 'uns into Another Dimensionwithout their gear to test their mettle, and doesn't stick around to watch (he had to go take on the Monster of the Week.) Our heroes very nearly wind up as a giant's breakfast. When they manage to get themselves out of it and return, Daggeron's "I never doubted their safe return" just doesn't ring true - you really feel like the writers threw the line in so that Daggeron wouldn't appear to be criminally irresponsible. To be fair, Daggeron appeared to have arranged the whole thing, since the giant was a vegetarian and he had conveniently given the green ranger an inane task of practicing the spell he would need over and over again. So either this trope or sloppy script work.
In Joan of Arcadia, God gave Joan her "assignments" with little to no concern about how Joan's activities would be perceived and reacted to by her family and friends. At least twice, Joan's life was directly endangered by her following God's orders.
The Vorlons on Babylon 5 acted like this was in force, and pretty much everyone went along with it for the first half (or so) of the show's run. As soon as the main characters start to question it, all hell breaks loose.
LOST: While there are numerous examples of characters in authority positions abusing their powers because they know everything will turn out alright, the straightest example of this trope is Jacob, the island's ageless supreme protector, who lives in isolation away from the people he brings to the island. His ultimate goal is to prove wrong the theory of his (currently) nameless archenemy, who thinks humans are inherently flawed with sin, and so he allows them to form their own ideas of good and bad on the island while avoiding corruption by the nemesis. If Jacob intervenes, so he believes, his theory will be worthless: they must make their own decisions without his guiding hand. Regardless, in getting characters to the island, he has exercised some moral license: allowing Sayid's wife Nadia to be killed or knowing the plane they intended to return to the island on would crash.
The Inquisitor, the villain of the Red Dwarf episode of the same name, behaved as though he has one. After surviving to the end of time, he concludes that there is no god and no afterlife, and that the only purpose of existence is to live a worthwhile life. To this end, he travels through time, deletes those he judges to have wasted their lives and replaces them with another possible version of themselves. An interesting twist, though, is that allows his victims to judge themselves, and the requirements aren't that stringent, especially if you have extremely low personal standards.
In a Fridge Brilliance moment, Daniel Jackson fits this trope. He's been to heaven and back, most of his ideas and choices are good, and he even has the right, power and morality justification to question ascended beings. Lampshaded later when he becomes a Prior and asks for a little cooperation for his latest plan (his CV should have spoken for himself). He's not, but he proves his worth and his loyalty, and his actions are still the ones saving the day. To a lesser extent, SG1 and Stargate Command is for the countries of Earth who don't profit as much from the technology as the US, and want to screw the ones that actually work in the process. They still do what they know best, and save the world(s) through it every time.
Rube in "Dead Like Me" seems to have this. In the pilot episode, he basically tells George to start taking people's souls, or else, without offering any explanation as to why. When she, quite understandably, refuses, the consequences are dire, and she is berated for doing what anyone with a conscience would have done.
Jor-El behaved this way on many occasions in Smallville.
The Great Dragon in Merlin has advised/ordered Merlin to do some incredibly dodgy stuff, including letting a child die and poisoning a terrified woman. Sometimes he obeys, sometimes he doesn't - but either way it usually it turns out bad for Merlin.
Religion and Mythology
A core tenet of almost all major religions is about God or gods having sovereignty over the universe and being allowed to do what they feel is right.
In Warhammer 40000, there's really no morality to speak of anywhere, but the Eldar are very fond of acting like this trope is in effect. Of course, it helps that they can see the future...
Some interpretations of the Ravenloft setting's Dark Powers invoke this trope, depicting them as harsh but well-intentioned judges who consign the multiverse's foulest villains to The Punishment. Too bad for innocent bystanders living in the domains which confine said villains, because they're left at the mercy of the punished, as are the poor saps who get dragged into the game-setting by the Mists.
In the Golden Sun games, the Wise One does this to the entire group at the end of The Lost Age by sending a three-headed dragon to stop them, and only after they defeat it do they learn that said dragon was actually Isaac's father and Felix and Jenna's parents, and are on the verge of dying as a result. But upon restoring the powers of Alchemy with the last Elemental Star, the three adults are healed miraculously. It's later revealed that the Wise One did this to test their virtue and dedication, so as to make sure that the power of Alchemy would not be misused (like they had been in the past) if they were revived.
The Wise One kind of dropped the ball there, since committing patricide probably tests as much for sociopathy as it does for virtue or dedication. If not more.
In Neverwinter Nights 2: Mask of The Betrayer, it gets... complicated due to a multi use. The former god of the dead Myrkul's actions (creating the spirit eater curse to punish a deciple who rejected his self believed license) comes from believing as a god he has one. If the player takes a specific coarse of action granting him an ironic, yet peaceful death, he chastises the player, accusing the player of believing they have an Omniscient Morality License "You have no right spirit eater, judgment is the purview of the gods". The new god of the dead's reason for doing the exact same thing as Myrkul, using a Fate Worse Than Death to punish people who don't worship gods, borders on this as well. Note: in Forgotten Realms canon, Myrkul is designated evil, and his replacement is neutral (i.e., not good).
Wilhelm in Xenosaga. Though he does show concern for the future of humanity, he has no concern for anyone who perishes during the course of his plans, even his closest allies, and sees all of life as a grand stage performance.
Subverted in Super Robot Wars Alpha 2, when the Guardian Goddess of Earth, Ganeden, lashed out at all the humans who decided to move into space and all the aliens. She then began erecting a dimensional barrier around the Earth. For that, the good guys tore her apart.
In Disgaea, Master Lamington manipulates Laharl's group, the EDF, Vulcanus, and even the Angels. Laharl calls him out. Very hard Of course, Lamington's motivations are not necessarily bad.
Disgaea4 delivers one in the form of the demons, who continually cast judgement on humans for being "bad", "sinful" and "warlike" and look down on them for becoming secular and not fearing demons enough anymore to provide them with the "fear energy" demons require (the fact that demons are essentially parasites living off humans is apparently lost on all the protagonists). There's also another with this universe's God who places genocide machines on every inhabited world in the universe and activates them when he feels like it. Not only is he indignant if the protagonists stop this happening to Earth, but if you get the ending where Valvatorez and co. actually defeat God's avatar in battle, the game ends with both Earth and it's Netherword being burned by God's forces.
In Mass Effect 1 and Mass Effect 2, the human-supremacist organisation Cerberus seems to think they operate under one of these, believing that any action they take to elevate humanity's position in the galactic community will be vindicated by history. On the one hand, they acted to prevent the release of a biological weapon on the Citadel, and tasked Shepard with stopping Collector attacks. On the other hand, they've conducted nightmarish experiments on aliens and humans, unleashed Thresher Maws and Husks on unsuspecting colonists, trained rachni as shock troops (which ultimately kill two marine companies), tortured children to make more powerful biotics, and "accidentally" detonated starships over colonies to infect unborn children with element zero (keep in mind that 30% develop fatal cancerous growths).
The protagonist of pretty much any Bioware game can be like this, given the amount of questionable or outright evil moral choices available. But the protagonist is the only person who can save the world/galaxy/kingdom/etc. and though you can get called out on it, you won't get sacked from universe saving for killing off half the races in a game and you will still ultimately be the hero.
Blaze Union: Good lord, Baretreenu. You want to Mind Rape someone to prove their innocence?! Why are you not getting called out on this?!
In Ōkami, Waka could very likely be accused of this trope, in the game, it's shown that he can see the future, and is pretty strong, at one point even fixing the coastline of it's corruption, staggeringly, he does very little in the way of progress, when, theoretically, he could fix most of Nippon's problems, and a lot of problems would probably have been solved if he took a more direct approach in saving the world, rather than let destiny play out.
Of course Waka, knowing the future, would know that he's not powerful enough to defeat the Big Bad without a powered-up Ammy's help.
The Menders of Ouroboros in City of Heroes. Their leader, Mender Silos, hails from near the end of time and has recruited the heroes and villains of the present to try to stave off a disaster in the near future, known only as The Coming Storm. No one ever tells you what this might be, and the Menders will send you to accomplish the most random, and sometimes morally questionable, tasks in hopes of preventing the Coming Storm. (Though, if you're a Villain that's hardly a problem.) To add to all this, in every story arc they give you, a mysterious messenger will leave you notes, telling you not to trust the Menders but to play along anyway. And the Menders also allow you to relive your past adventures, just in case you missed a badge or reward of some kind.
.hack//G.U. Games: Ovan, full stop. He puts Shino in a coma and enables Sakaki to Mind Rape people and attempt to take over the world. Why does he do all this? So that Haseo will be able to stop AIDA.
In the Myth Arc of the Assassin's Creed series, The Ones Who Came Before are capable of apparently perfect precognition, yet bore witness to the near absolute destruction of their First Civilization on Earth 75,000 years ago thanks to a solar flare. Dying out due to underpopulation, they Fling A Light Into The Future by manipulating the course of history such that the modern day Assassins can use their Lost Technology to attempt to avert a recurrence of the same catastrophe in 2012. Thousands of years of war, betrayals, scheming, and suffering as the Assassins battle the Templars for control of the future of humanity are part of this scheme, but they have no choice when the alternative is potentially the extinction of the human race.
The end of the third game reveals that Juno at least doesn't really care about humanity at all. She's been manipulating everyone to facilitate her own return and bid for conquest.
Dan: And here I thought you did it all because you were an insane sadist...
Fa'lina: Well that too! But that comes with semi-omnipotence also!
Despite being The Hero (or, some would argue, the Designated Hero), Dominic Deegan: Oracle for Hire's eponymous main character has often invoked this trope to justify his morally questionable or just plain ridiculous methods of defeating the villain, especially after his Power Creep starts setting in after the Storm of Souls arc.
He got called out on it after the Snowsong arc with the Supergreg silliness, and made to do community service, for solving a problem by manipulating everybody. He could have solved it conventionally, but that would have damaged his ability to Save the Villain.
Most of the time he's actually pretty straightforward about his moving-people-around-the-board ploys; given his ability to confront problems that exist anywhere besides the psychoplanes almost always consists of 'knowing more than anyone else' and 'communicating with people,' he has to do his part by networking.
Rillian the Necromancer has it much worse. The part where he followed Dominic and Luna around on their vacation in disguise, putting them through tests and ready to kill Dominic if he 'failed' and his mind broke stands out particularly: worked out great, possibly necessary, appalling in principle.
Boband George one of the earliest noted sprite comics, frequently invokes this. The Author at times either personally deals with (or at the very least addresses to the cast and audience) problems that he created for the sake of the series. Needless to say at various points in the comic, this pisses off the heroes but is played for laughs. Sprite Comics that were directly inspired by B&G tend to either follow this example or allude to it, especially earlier comics, or those made by "Noobs"
Schlock Mercenary features a super-intelligent AI which epitomizes this trope. He could probably solve the universe's problems if he didn't think it was better for everyone to "work things out themselves".
Petey may be god-like within the galaxy, but he is engaged in an out-matched war with the dark matter beings from Andromeda, and an "easy fix" such as breaking through a teraport shield to save a single ship could cost a star system in the larger conflict. Petey increasingly sticks to behind-the-scenes work to conserve resources.
One of the students at PS238 has an ability that can best be described as hypercognition, an ability to form connections and make deductions that completely ignore quantum uncertainty and chaos theory. This leads to doing no small amount of questionable acts.
Tom Davidson, who can Time Travel, has much the same deal going on.
Sarda the Sage from 8-bit Theater subverts this trope, with White Mage convinced he's operating under this license while the "Light" Warriors know damn well he hates them (and now they even know why).
The Great Bird Conspiracy of Kevin & Kell, in addition to manipulating the inner workings of government and other institutions, carried out a long-running plan to prevent society from destroying itself by establishing computers to run it. In order to accomplish it, they abduct Vin, Fenton and Ray and have them work for Microtalon when they find out too much about it, and cause Lindesfarne to believe that her boyfriend Fenton is dead. While the people in question are eventually returned with their memories of their time at Microtalon wiped this caused a considerable amount of anguish for the cast. Not to mention the fact that the birds were responsible for making all these species intelligent in the first place.
Misfile features a clever subversion with God himself, who is all-knowing and yet apparently allows his angelic underlings to get away with errors. However, the twist (which is implied) is that God knows that these errors, such as the titular misfile, result in more actual good than harm, making him one hell of a chessmaster...
The Wizard of Oz example is lampshaded in Cheshire Crossing when Dorothy finally confronts Glinda the Good Witch with the accusation that Glinda deliberately withheld information about the ruby slippers to get Dorothy to murder the Wicked Witch.
Doc Scratch of Homestuck, who actually is just about as close to omniscient as it's possible to get in his universe, certainly sees himself has having this. His response to being called out on it by Rose is as follows:
Lies of omission do not exist. The concept is a very human one. It is the product of your story writing again. You have written a story about the truth, making emotional demands of it, and in particular, of those in possession of it. Your demands are based on a feeling of entitlement to the facts, which is very childish. You can never know all of the facts. Only I can. And since it's impossible for me to reveal all facts to you, it is my discretion alone that decides which facts will be revealed in the finite time we have. One can make either true statements or false statements about reality. All of the statements I make are true.
And subverted because Doc Scratch is genuinely evil.
Chris the producer from Sailor Sun: Turning his lead actor into an actress with an illegal transformation device just to lend his Gender Bender story authenticity? check. Deliberately getting her knocked up just so he can steal her Kid from the Future? Check. Stealing another alternate version of the Kid from another future when she proves unable to support the first one? check. Using a time portal to further screw with her life, either for the drama or just for the lulz?
It seems that the Predictamancers from Erfworld have a disturbing tendency to lean toward this.
On one hand, Fate is a literal cosmic force, and whatever the Predictamancers predict will come true, by definition. (Whether the Predictamancers tell the real predictions are a whole other story.)
On the other hand, both of the introduced Predictamancers have an annoyingly vague approach to telling their predictions, and give little to no help for anyone featured in their predictions, instead preferring to try and manipulate things from the side.
Played perhaps uncomfortably straight with the Tao in the Whateley Universe, which ostensibly always knows just what is required to maintain 'the balance'. So far a few people have coughed but only Strawmen have actually debated against it.
From the Global Guardians PBEM Universe, the clairvoyant Domino, one of the closest advisors of criminal mastermind Baron Samedi (and one of the reasons the Baron is so successful) has this attitude. She knows the future (and the present, and the past) from her perfect tarot-card readings.
Aang: I can't just go around wiping out people I don't like! Sokka: Sure you can. You're the Avatar!
Danny Phantom had Clockwork and the Observants. Clockwork's reaction to Danny's evilfuture where he's a mass-murdering, rampaging sadistic sociopath? "So he's the strongest, most evil ghost in the Ghost Zone. So what." No wonder some fans think him to be evil. Clockwork has the advantage of knowing everything, or at least all the outcomes. It's in his Catch Phrase. The fact that he never used his knowledge for outright good or evil shows that he's being neutral about using his phenomenal cosmic power.
That said, he does ultimately help the heroes stop Dark Danny and becomes Dark Danny's jailor.
A mild version of this can be found in Time Squad: to prevent history from "unweaving", the crew needs to engage in some morally objectionable actions (making Edgar Allan Poe have a mental breakdown, create mutual tension between the Hatfields and the McCoys, etc.)
Subverted in Yin Yang Yo, when a Lie Fairy creates a villain that grows every time Yin and Yang lie. At the end, she shows up and congratulates them on learning their lesson... only to have the townspeople angrily point out that she destroyed the city in the process.
The eponymous Pagemaster takes a cowardly child and subjects him to all sorts of deadly situations. To all appearances, there was a real chance that the kid would either die or develop severe mental trauma as a result of this. But instead he learns to be courageous, and the Pagemaster gets off the hook because apparently he's just so darn wise that he knew it would work out like this from the beginning.