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First game's Andrew Ryan founded the underwater city of Rapture to be an Objectivist utopia, where personal freedom and self-advancement were valued above all else. However, Ryan's desire to keep his city an Objectivist utopia eventually led to him taking dictatorial control over the city to prevent it from falling into the hands of his (much more competent) competition... exactly the way his own theory said it ought to.
Ryan is more of a subversion, especially when one considers the very likely idea that he's taken Objectivism to its logical if excessive conclusion: that he did everything for his own benefit. Add in the point of altruism being considered anathema to personal self-interest and the emphasis on "looking out for number one," it becomes clears that Rapture wasn't meant to be a charitable refuge for the world's elite. In other words he isor rather was Rapture and that all that mattered to him was ''himself.'' Everyone else in the city was simply invited to try their luck in his glorified playpen.
BioShock 2 has Sofia Lamb, who is even worse than Andrew Ryan. She is an extremely outspoken collectivist who preaches that man needs to ignore his selfish desires to advance the greater good (the exact opposite ideals of Ryan). Yet many of her actions are essentially pushing her own beliefs onto others, diverting blame away from herself, refusing to admit she might be wrong, and rarely listens to other's ideas. This makes her a very self centered and biased woman who has a superiority complex with the very flaws she preaches against. Granted, she admits that she is flawed and has biases, yet she remains blind to how contradictory her words and her horrible actions really are.
The dwarves in Chrono Cross hate humans for their genocidal, polluting ways. They also commit genocide against the faeries and fight using filthy, smoke-spewing tanks. That the game doesn't recognize the contradiction here is one of the major dividing points in its fanbase.
The Global Liberation Army in Command & Conquer: Generals are pretty much this trope. At first, they scream incessantly about oppression, imperialism, and how just they are. Other comments, however, underscore that they're basically ill-tempered, sadistic, sociopathic low-lifes to a man, and have no problem in killing civilians to get what they want. Except for the lowly Workers, who are some of the single most hilariously down-trodden, abused schmucks in gaming history.
Disgaea 3 - Super Hero Aurum is a gigantic hypocrite. He kills a nice guy, imposes as a loyal butler, and messes up the next two hundred years of Mao's life to raise him as a cruel and wicked overlord, and all so he (Aurum, that is) could have a truly evil villain to fight. He even abuses his number one fan with a death curse while the poor lad remains painfully oblivious to the fact his mentor betrayed him up until the last moment. By the time Mao turns things around (if he does turn things around), the entirety of his party is more than ready to tear him a new one for committing hypocritically evil acts on such a grand scale.
Aurum has gone pretty much insane from being absurdly powerful and having nobody to fight for hundreds of years, and doesn't seem to be able to die after having absorbed the powers of so many evil gods. Of course, gaining evil powers isn't good for your psyche either.
In Dragon Age II Knight-Commander Meredith sees magic as a curse, and mages as a major threat to her city who must be contained at all costs. So she uses an ancient magical artifact to give herself magical superpowers and animate statues to indiscriminately attack people in the final battle.
The same could be said about Anders, who accuses her of going too far in her treatment of mages as dangerous people, yet he proves just how dangerous and obsessed he himself is - ask the people in the Chantry he blew up. Not exactly the strongest point in making mages seem like all the other people.
And Fenris believes Mages are too powerful to be trusted and will inevitably abuse their power, so they should accept being enslaved and controlled by the Chantry. He himself is an escaped slave with magical powers who is being hunted by his former master and will mercilessly kill those who are no longer a threat to him if they piss him off enough. Like Meredith he has a massive Freudian Excuse, but it gets a little old when he spouts out reasons for mistreating mages that could just as easily apply to him. Anders calls him out on this.
Dishonoured has High Overseer Campbell. Despite being the head of a religious organisation dedicated to rooting out the practice of black magic and The Outsider worship, he maintains a secret room full of books detailing spells, as well as an Outsider rune. His room also contains discarded lady's undergarments and notes from a nearby brothel, despite preaching of virtue and temperance. Although, the brothel is where Lady Emily is being held, but it does mention that he likes being there to sample in their services while keeping an eye on Emily. In fact, that probably hints on something even worse about Campbell.
Caesar is an Evil Luddite who considers over-dependence on technology to be a sign of weakness, and forbids the use of any medicine more complicated than healing powder (a concoction of medicinal herbs). This has resulted in thousands dying in his empire due to improper medical care, which he dismisses because apparently they were too weak to live. However, he keeps a broken Auto-Doc in his tent and, if the courier sides with him, commands the courier to fix it so it can cure him of a brain tumour. Plus his Elite Mooks get to use more technologically advanced weapons than the lower ranking members.
Caesar's Legion generally has tons of this. Firstly, they preach at how important loyalty is (in fact, it's the reason they butcheredNipton) but constantly betray their allies, in fact betraying and assimilating their allies is practically their official policy. Secondly, the Legion is strongly opposed to drugs, but Hydra can occasionally be found on the bodies of dead legionnaires, and it's implied that they manufacture drugs themselves.
Ulysses, from the Lonesome Road DLC, invites the Courier to the Divide so he can deliver a massive What the Hell, Hero? about how actions can have unforeseen consequences (A package the courier delivered to the Divide detonated the nukes that were stored there and completely wrecked the place). But playing through the other three DLC will show that Ulysses himself has caused plenty of chaos throughout the Wasteland, often as an indirect consequence of his actions: He led the White Legs during the sacking of New Canaan, which was just as prosperous as the town the Courier accidentally destroyed, and he trained them and gave them machine guns, allowing them to become the major antagonists of Honest Hearts. He almost released the Think-Tank from their imprisonment in Big MT by asking them an Armor-Piercing Question. And he told Elijah the location of the Sierra Madre, setting in motion the events of Dead Money, which results in dozens of people getting kidnapped and murdered and the entire continent nearly being drowned under poison gas as part of Elijah's plan. Unfortunately, since the DLC aren't programmed to interact with each other, there's no way to call him out on this.
Elijah is a huge example in Dead Money. For example, he'll talk down to you for using a Pip-Boy, saying that it dulls your brain... but you can clearly see him using a Pip-Boy himself. He expresses amazement at how many people he's been forced to kill because they let their greed for the Sierra Madre's treasure get the better of them and compromised his plans, not realising that he's suffering the same obsession as they were.
He also criticizes his previous captives for trying to take advantage of each other and killing each other when they've outlived their usefulness, necessitating the linked collars, yet once you get into the Villa, he suggests you kill off your now useless team. And once you open the Vault (unless you're evil and make a deal with him) he'll come down to kill you himself.
Salt-Upon-Wounds, leader of the White Legs from Honest Hearts, says that he and his tribe are are honorable and strong warriors, but he'll beg for mercy if Joshua Graham shows up, kills all his warriors, and holds him at gunpoint. Even worse, he says that Joshua Graham is crazy because "he kill all White Legs", even though Salt-Upon-Wounds ordered the slaughter of every man, woman, and child in New Canaan- Joshua Graham's hometown.
Fate/stay night - Saber, who is basically female Shirou with less delusions, as a heroic example. Archer is the one to call her out on her treatment of Shirou's ideal by pointing out that her wish is the same as his only 'more so.' Tohsaka also realizes she cannot really lecture Shirou anymore when she finds herself making the same kinds of choices and is unable to kill Sakura, despite the cold pragmatic value that doing so would have.
In Final Fantasy X the Church of Yevon preaches that all machina (advanced technology) is blasphemous and the reason for Sin's existence. Yet they have no compunctions with using machina weapons themselves. Learning this while exploring the church headquarters in Bevelle is essentially the final straw that causes the party to lose all faith in the church.
Wakka: These machines are abominations against Yevon!
Seymour: Then pretend you didn't see them.
Wakka: ...That's not something a maester would say!
Francis McReary from Grand Theft Auto IV the Deputy Police Commissioner of Liberty City, who honestly believes that his status and position automatically make him a morally just person and acquits him of any crimes that he commits. You quickly see past this facade when he orders you to gun down people by the dozens in order to hide his corruption and more importantly, when he orders you to gun down his own brother to save his career.
Grand Theft Auto V: Michael and Trevor. Michael is a backstabber who criticizes other backstabbers (a gold digger who gave him ten bucks and an autograph for cleaning up her sabotage of her husband's vehicle, and his psychiatrist for ratting him out after getting paid in the hundreds of thousands), and Trevor criticizes Michael for his betrayal of friendship, even after brutally killing his best friend's cousin and said cousin's fiancee for pissing him off, and selling people to a cult. Neither of them are very morally conflicted about this, as seen in this exchange.
Trevor: Jesus, your therapist has a lot to answer for.
Michael: I know, I still hate myself. But hey, at least I know the words for it now.
Trevor: Yeah, but I hate you, and I know the words for it, so does that mean I don't have to go to therapy-
Franklin: Hey, look, you two motherfuckers terrify me of that middle-age.
The Ascalonians of Guild Wars, and particularly Gwen, decry the Charr for destroying their country and killing most of them. Unfortunately, they then go on to try to commit genocide against the Charr. Since the RPG elements of Guild Wars Nightfall are gone by EotN, the player has no real choice but to go along with it.
The Charr in Guild Wars 2 have their fair share of hypocrisy. They refer to the humans as cowardly and dishonorable for using artifacts like the Foefire and Stormcaller to rain magic down upon the Charr, but then turn around and praise the Searing despite it doing the same thing. Furthermore, the Charr like to rub it in the other races' (particularly the humans') faces about how they retook their ancestral homeland and have no need for gods. All the while, they conveniently forget that the Searing, which is largely what allowed them to conquer Ascalon in the first place, was the work of the now hated Flame Legion and the false gods they worshiped.
Kreia of Knights Of The Old Republic II will talk about how arrogant and closed minded the Jedi are and how they should be more open to other people's ideas. Of course, if you then point out flaws in her philosophy, she'll dismiss you as incapable of understanding it.
In addition, Kreia despises The Force and those who are dependent on it, and seeks to destroy it. However, all of her attacks and scheming are dependent on the Force, and she's too physically frail to fight otherwise. If the player calls her on this, she claims that it's because being intimate with the Force gives greater insight on how to destroy it. But to her credit, she does concede that the player makes a good point, and may very well be right.
She's got nothing on Atris though. Atris is an immensely Holier Than ThouKnight Templar that smugly insists in being the last true jedi left. She even wanted the exile executed for defecting to Revan. Even Bastila didn't o that far. She also completely fail to realize that her absolutism has corrupted her to the dark side long ago. It takes Kreia to convince her otherwise.
Khalisah bint Sinan Al-Jilani in Mass Effect has shown an extremely strong pro-human and anti-alien bias from Shepard's conversations with her in both games, so it may come as a surprise to see her kissing and embracing an asari in a few select data files in Lair of the Shadow Broker.
In Lair of the Shadow BrokerTela Vasir calls Shepard a hypocrite for judging her dealing with the Shadow Broker when s/he's working with the terrorist organization, Cerberus right before she dies. She has a point if you're playing a full Renegade Shepard, who will endorse Cerberus' actions. Paragon Shepard not so much; they see working with Cerberus as a Necessary Evil at best and will betray it in the end, if s/he hasn't done so already.
Ronald Taylor, Jacob's father, taught his son that a man always admits to his mistakes. On Jacob's loyalty mission, we find out that Ronald has turned the Hugo Gernsback and his crew into his own personal kingdom and thoroughly doesn't own up to everything that he's been doing.
And then, there's the coup de grace of this universe: the asari, the most technologically advanced Council race. They make a law stating that anyone who withholds Prothean technology will be fined severely and the tech will be taken from them, with extreme force if necessary, so it can be shared with the galaxy at large. Then the third game reveals that they have possibly the only intact Prothean beacon in existence. Obviously, this gives them a massive advantage, especially considering they've had it since their Stone Age and hid it in an ancient temple.
Harbinger derides the asari as inferior for relying on other species to reproduce. Guess what the Reapers need to make more Reapers?
Mass Effect 3 has Kai Leng, who brags about how either Thane or Kirrahe died like cowards if he killed them yet in the game repeatedly proves that he's a Dirty Coward who relies more on firepower or manpower rather than personal skill when confronting Shepard and tends to run whenever things go south for him. Not to mention that they went down fighting. Leng's last act? Trying to stab Shepard while his/her back is turned.
In an unusually tragic example of this, Shepard at one point berates James Vega for the Death Seeker tendencies he shows, despite having become somewhat of a Death Seeker him/herself by this time.
In Megaman Battle Network 4, Duo seeks to destroy the earth because humans are wicked. For some reason, the morality of destroying an entire planet is never brought up, despite being painfully obvious to the player.
Pokémon Black and White has Ghetsis, who claims N is a freak without a human heart, when it was Ghetsis who was manipulating N the whole time. N is his son. Cheren and Alder do note this, though. N was only trying to do what he felt was right, but Ghetsis is a self-serving monster.
We also have Team Plasma in general who fight for the freedom of Pokemon while at the same time abuse the Pokemon they catch when nobody's looking.
Or when it's just you and your close friends looking. Who kicks a Munna?
In fact, N seems to be the only member of Team Plasma who is not a hypocrite, at least until Pokémon Black 2 and White 2. In that game, he is the leader of a splinter group of Plasma with more noble goals that opposes the current group.
N did however has his own team of Pokemon despite being against catching them and using them for battles.
N's pokemon are always local, implying that he always releases them back to their homes after facing you. In addition, he admits to the practice, saying that the only way to change the system is to reach the top of it (that is, become League champion, and then, presumably, disband it).
Pokémon X and Y has Lysandre. He hates thieves, liars, and selfish people. Who does he hire? Team Flare; a group that is made up of all the very people he claims to hate and he wants to blow up the world and start it over with THESE people. He's either really stupid or this trope. Not to mention that he steals a bunch of pokeballs from the Pokeball Factory. What's worse? No one ever calls him out on it.
Federal Agent Edgar Ross constantly derides John Marston about how Marston was (and, as Ross sees it, still is) a criminal, never letting up on how morally superior he is because Marston kills people. Although, Ross never seems to make the connection that Marston is only killing people now because Ross has taken his wife and son hostage and is forcing him to hunt down the members of his old gang. And whats more, it was Ross' job to bring in those men, so he's basically having Marston do his job for him. And then, when Marston has fulfilled his end of the bargain and goes back to living peacefully on his ranch with his family, Ross sends the army to kill them anyway.
In Shin Megami Tensei I, the Chaos Hero (one of the main hero's companions) leaves the group after defeating his nemesis Ozawa, since now that he's finally acquired real power, you'll just hold him back and slow him down. Nevermind that you've carried him for most of the game until this point, saved him, helped him get out of the afterlife and back to the living world, AND that his precious new power stems from him stealing your most powerful demon and fusing with it.
Each of the Reason-bearers in Shin Megami Tensei III: Nocturne is a hypocrite who violates the philosophy they subscribe to in some way. The philosophy of Shijima preaches of The Evils of Free Will and decries human ambition as destructive, yet its most vocal advocate, Hikawa, is a highly ambitious Übermensch who's prepared to trigger the apocalypse to see his goals reach fruition. Chiaki preaches the philosophy of Yosuga, in which the strong have absolute power and the weak are subjugated or killed, despite being a relatively weak individual who only gains power when a much stronger entity sympathises with her and offers her a Deal with the Devil. Isamu's philosophy of Musubi states that all beings must be isolated from each other and free to pursue their own ideals without interference from others, yet Isamu is ineffective at accomplishing anything for himself and only succeeds when he gets others to do his dirty work for him.
In S.T.A.L.K.E.R., the Duty faction preaches about the horrific dangers of the Zone and why it must be contained from spreading over to the whole world. Yet, in Call of Pripyat, a quest involves you investigating a strange anomaly at an abandoned water cooling station northwest of the Yanov train station. The quest requires you to secure a special detector from the wrecked ship in the first map. Once you have it and use it, the anomaly spits out the bodies of now lifeless Duty stalkers down to the ground. Among them is the original founder of the faction. His PDA reveals that the faction was originally comprised of soldiers and SFOs from the Ukrainian Security Service (AKA the Ukrainian military) sent out to the Zone to secure it from unauthorized personnel. According to the backstory, his unit was on a particularly risky expedition of unknown caliber when a sudden blowout wiped out almost his entire unit. Shaken by this upheaval, the Captain (AKA the founder, who is only known as Tachenko) of the unit staged a communications breakdown and ordered his troops to go rogue from the USS and join the other stalkers for opportunistic jobs in the Zone. His ploy proved successful even though he also inadvertently caused chaos within his unit. The Captain and his subordinates managed to silence this debacle and continued on with impunity. Then, one day, he and three others with his group traveled to the water cooling station and end up getting trapped in the anomaly that you discover in this game. His group disintegrated under tragic circumstances and Captain Tachenko, by then self-promoted to General, became Driven to Suicide. The rest of the unit legally declared Tachenko MIA, and by then had recently appointed General Krylov (from Clear Sky) to assume leadership of the unit and he turned it into the now supposedly adamant Knight Templar faction that we know presently. After hearing the little story in the founder's PDA, you can choose whether to give it to Duty, Freedom, or the trader in the wrecked ship. Giving the PDA to the Freedom leader will cause him to blissfully call out Duty for being a bunch of frauds acting like every other greedy and selfish stalker out there in the Zone. Had this anomaly not occurred and had disappeared in the game or had the PDA's data gotten erased, Duty's dirtiest secret would have never been discovered in the first place and that bit of information would have more likely to be found in the game manual which no player these days would even bother.
In Suikoden V Gizel Godwin informs his young wife Queen Lymsleia that her brother is raising an army against them and refers to him as a traitor. Lym angrily points out that Gizel staged a coup of the palace and caused the deaths of her parents and that he was the traitor.
Tales of Symphonia gives us Mizuho, a village of ninjas who have an entire culture built around spying on everyone on the planet for seemingly no reason at all, yet completely flip when someone spies on them.
There is really no excuse for the exchange with Pharoh though, where Yuri responds to Pharoh's use of the exact same logic, right down to the wording, that Yuri used to justify his own vigilantism with;
Captain Vor tries to call you out for not fighting with honour. The charge rings hollow given that he uses Teleport Spam and mines and springs flunkies on you.
Some of Sgt. Nef Anyo's taunts include mocking the Tenno's fashion sense (while wearing a giant shoebox/trashcan on his head) and challenging them to face him (often while cloaking and running away).
Sylvanas Windrunner in World of Warcraft makes a big deal over how she and her followers the Forsaken were raised as undead against their will and forced to serve the Lich King. The moment she gains access to the power to create new Forsaken, she sets about a campaign of murdering every human in the Eastern Kingdoms to raise as new Forsaken who are forced to serve her.
The short story Edge of Night seems to indicate that she no longer views undeath as such a bad thing compared to The Nothing After Death, especially not when she had visions of the Forsaken dying out after her death. There is a reason for her change of heart regarding raising the dead, albeit not necessairly a good one.
Taran Zhu constantly derides the Alliance and Horde conflict as being fuel for the Sha, only to later fall victim to the Sha of Hatred himself. After the players Beat the Curse Out of Him he does acknowledge his own shortcomings, but his views on the Alliance and Horde don't change.
Zhu also enlists Horde and Alliance heroes in wars of extermination against the Yaungol, Mantid, and Mogu, while continuing to berate them for their "race war" that he does not understand and declares that he has no need to understand.
The X-Universe series has Space Fuel (AKA Argon Whiskey), an alcoholic beverage that is declared contraband in Commonwealth space. Yet, in the Argon sectors of Herron's Nebula and Nyana's Hideout, two distilleries can be seen there and their goods can be bought. Even more jarring is that every Argon shipyard has them in stock and they actually allow you to buy one of them for personal use. One wonders why the Commonwealth haven't put a blacklist on the purchasing and sale of distilleries when an easy loophole can be exploited by potential fixers. Needless to say, this makes trading with pirates easier as long as no combat missions are performed against them and that the distillery in question is built on non-Commonwealth space.