Mike in the Web GameCreepo's Tales: Chopping Mall. While he does want to solve the mystery of the parking-lot disappearances, it's explicitly out of Pragmatic Hero-ism (being a hero would give him enough publicity to help his failing business) instead of altruism per se. And during the game, his actions include breaking-and-entering, double-poisoning a business rival's clerk via Nausea Fuel-rigged burger and water, and stealing classified police intel. Oh, and in the ending? After discovering that the aforementioned rival is the one causing said disappearances in order To Serve Man, Mike kills said rival in self-defense... but then invokes Slasher Smile and ends up serving his body to Mike's customers, meaning that Mike is literally Not So Different from the cannibalistic Serial Killer.
In Mobile Phone GameCutie Riot, quest dialog mentions the player is outright killing people when completing quests, due to the player's mother being killed by monsters.
Tales of Vesperia plays this trope interestingly: Flynn isn't unsympathetic nor completely ineffectual, it's just that he keeps being lauded for feats and accomplishments that were actually done by Yuri and Brave Vesperia, making it a literal case of "Designated" Hero. His issues over this are what lead to the requisite Tales SeriesDuel Boss fight against him.
Yuri himself is considered by some to be this: a hero with a bizarre, inconsistent, "it's okay when I do it" moral code; and rarely if every being called out on his inconsistencies. Whether you agree largely seems to depend on whether or not you think the writers did it intentionally or not (or if you consider his inconsistencies as being incredibly subtle character development).
Pretty much the entire party in Tales of the Abyss falls under this due to a simple, spoilered fact Luke, the one they land the most blame on and spend a good chunk of time berating over his various failures, is actually seven. Add to that all the secrets so many of them know, the fact a good chunk were pegging on to the spoilered fact for some time before The Reveal and Wham Episode, and they tend to not look much better than the Anti-Villain bad guys they face off against.
Reimu Hakurei can definitely fall into this category. Reimu often only saves the day (if you don't let Marisa do it instead) because she's forced to do it, since she's the only one who can (except Marisa), and the one people can pressure into solving problems more easily. Sometimes, however, like Mountain of Faith, Reimu attacks people she knows are not doing anything bad, and are actually goddesses just trying to carve out a niche for themselves (mind, their methods are dangerous to Gensokyo as a whole, not that they knew). In Undefined Fantastic Object, you can explicitly choose for Reimu to go "investigate" the treasure ship not because she is worried about Gensokyo, but because she wants to loot the treasure. Later games and additional material give her a grudgingly growing social conscience, slowly making her more receptive to the needs and wishes of both humans and youkai.
The Cute Witch and The Rival, Marisa Kirisame, falls even more into this trope, as an unabashed Kleptomaniac Hero who often saves the world by accident while trying to loot the final boss's house for valuables. In Imperishable Night, she even outright introduces herself to the Big Bad as a "burglar", much to her partner's dismay (who was actually trying to stop the Big Bad, and talked Marisa into helping her do it).
The protagonist of Road Avenger, who causes what is probably millions of dollars in collateral damage and kills a few innocent people in his attempt to avenge the death of his wife, which was caused by him swerving into a rock in the desert to avoid the chaotic biker villains.
Some storylines are well-supported by lore and interwoven into the game in every way possible, but others are just Excuse Plots to loot gear from a new type of enemies in a new setting. For example, in the Mana Tombs dungeon, the enemies that Player Characters fight are simply graverobbers. Players fight them as mercenaries on behalf of a rival trade consortium. Graverobbers are obviously not nice people, but they're hardly the Legion of Doom players are supposed to be fighting across that ruined world. Meanwhile, the major "good" factions, the Alliance and the Horde, are openly examples of Gray and Grey Morality.
This is actually lampshaded by a new rare spawn mob in Duskwood, who questions why graverobbers like her are considered absolute scum, while the player character she's fighting has most likely looted the gear and weapons they're wearing right now from a dead body.
It's lampshaded at some point, but then ignored again. You get hunting quests in more than one place from a dwarf called Nesingwary and his son to kill various kinds of animals for gear rewards. Then in Northrend, Nesingwary's minions are evil poachers who massacre animals and whom you have to kill in turn for some druids. These "loot-crazed" hunters have dialogue indicating that they're trying to collect 20 Bear Asses to get some new piece of gear as a reward, just like you did. And then you can meet Nesingwary himself again in a different area, and he dismisses all moral questions in passing with one sentence and sends you out on his quests again.
Alphonse Lohrer in Tactics Ogre: The Knight of Lodis in that he works for the evil Lodis Empire that seeks to take control of the island of Ovis even though he does question Rictor's motive of taking the spear Longicolnis for the Empire. He is revealed to be Lancelot Tartare, a main antagonist in the next chapter, Let Us Cling Together.
Played With in Baten Kaitos. Kalas is a complete Jerkass for a good portion of the game, and he only helps people when it coincides with his interests. Then, a little over halfway through the game, it's revealed that he was Evil All Along. After you fight him, however, he pulls a Heel–Face Turn and spends the rest of the game as a much better person.
The Argon Federation in X3: Albion Prelude. We're supposed to think they're the good guys, even though, for all the information the game gives us, the Terran Conflict turning into a hot war was entirely their fault: an Argon character from X3: Reunion suicide-bombed Earth's Torus Aeternal, killing millions of Terrans instantly (let alone the people killed by deorbiting debris). This was a 30th century equivalent of 9/11 taken Up to Eleven; the Terrans' current Roaring Rampage of Revenge is self-defense.
However, a rather extreme case of All There in the Manual turns it into a rather dark shade of Grey and Gray Morality. According to the encyclopedia in the X-Superbox, over the preceding decade the Terrans had deployed a spy network into the Community of Planets with the intent of influencing the future course of their governments. This network was eventually discovered by the Argon Secret Service and the Federation understandably considered it an act of war. The Terrans' edge in military technology forced the Argon to take drastic measures such as artificially intelligent warships in order to give their navy a fighting chance. Since the Torus partly served as a shipyard and orbital defense station for Earth, destroying it opened the way for the Argon to attack Earth directly. It's still an atrocity, but at least it makes military sense.
Nilin of Remember Me, the noble terrorist who kills her way through Neo-Paris on the word of someone she's never met, even after declaring how much she doesn't like or trust him. She ends the game having released all the stored memories in the Memoreyes database to their owners, declaring that we need our memories, even the painful ones, to be ourselves... except she also declares she has the power to play God by editing people's memories to be whatever she wants, at least one instance of which being implied to result in the bombing of a hospital.
While Mike Dawson of the first Dark Seed was a competent hero, he has gotten so much worse in the sequel. He is whiny, constantly asking awkward questions, comes of as a Man-Child at some parts, starts to act unjustifiably antagonistic near the end of the game (and has dialogue choices to make him come off as even worse of a human being), and cannot win simple carnival games without cheating! At one point, Mike even unintentionally lets a man die through his incompetence by not bringing him his medicine because he was too weak to push the anvil off its cooler and too dumb to just ask somebody to give him a hand with lifting it. And this is supposed to be the good guy. It has even been theorized that the dev team may have it in for the real Mike Dawson and made him a Loser Protagonist on purpose. To be fair, he does succeed in his quest, but the ending leaves it all ambiguous. Make of that what you will.
Jake from Ride to Hell: Retribution. At one point, he murders several truckers to steal their truck, runs over two dozen police officers, and kills everyone in a power plant just to cause an explosion with the truck to let him jump over an electric fence. The story treats him as, at worst, an Anti-Hero.
This trope applies to the version of 50 Cent portrayed in 50 Cent: Blood on the Sand. Despite presumably being a multimillionaire he uses the fact that he wasn't paid for a concert as justification for shooting, exploding and murdering his way through an already war-torn country to try and recover a jewel-encrusted human skull. He behaves like a foul-mouthed thug at all times and is rude and threatening to every character he meets, even the ones who are trying to help him. The game has a special button just for spewing profanity at his victims. At the end he recovers the skull, sticks a cigar in its teeth and calls it an ugly bitch.
The title character of Hopkins FBI is described as a "modern day hero and full time righter-of-wrongs" on the back of the game package and his fellow law enforcers congratulate him for his work. In reality, Hopkins is a buffoon who botches a hostage negotiation, commits several crimes of his own such as theft and vandalism, fails to follow proper law enforcement procedure at any point, and gets several innocents killed from his own stupid mistakes. This culminates in him falling for the most obvious trap imaginable and accidentally killing his own girlfriend as a result.
In the Retsupurae video MST series for this game, the video where the spoiler-hidden event happens is actually called "Our Hero, Ladies and Gentlemen."
Marche Raidiju from Final Fantasy Tactics Advance. After finding himself in a fantasy world, he searches for a way home, and the only apparent way back seems to involve turning the entire world back, even though his friends and brother don't want to go. Over time, as Marche progresses on his quest, the others come around to his way of thinking and decide to go back, but Marche essentially making the decision for them at first rubbed some players the wrong way.
The Rockstar game State of Emergency was originally supposed to center around an amoral character who incites riots and freely takes part in destruction, mayhem and death. Rockstar, perhaps in trying to head off controversy, decided to switch the premise to a band of proletariat heroes fighting For Great Justice against an evil Mega Corp.... Without making any changes to the core gameplay of destroying property and killing hundreds of people. One GameFAQs user review explains the problem quite well:
Of course, there's some lame attempt at a story to justify killing dozens of law enforcement officers, namely that these are BAD law enforcement officers. They're corrupt law enforcement officers, and they need to die to release the grasp of the corporations on mainstream America in the future. Just like 1984, minus the hair bands. Unfortunately, the story is incredibly poor as it is, and feels only like an afterthought to make people think that the targets of your violence are deserving of it. Like when you throw a grenade into an unquestionably evil-owned restaurant.
Adam, of Metroid: Other M, became this for about 90% of players. Samus is treated as being in the wrong for leaving his command prior to the start of the game, and the events of the game are supposedly a means of redeeming herself, but the game never explains why quitting a job she disliked was some kind of irreparable black mark. Despite supposedly viewing Samus as like a surrogate daughter, he then treats her with emotions that vary from callous disregard to outright abusive behavior. He threatens to court-marshal Samus if she disobeys him, despite her being an independent agent (and "disobeys", to Adam, evidently includes "uses any kind of equipment I have not explicitly authorized you to use, even if it's protective gear"). One of his last acts is to shoot Samus in the back while a hungry Metroid is within arm's reach of her, solely to keep her from going into Sector Zero... as opposed to, you know, asking her nicely. It's quite an accomplishment that he can sacrifice himself to save Samus and still make it seem unforgivably dickish.
Tomb Raider: Lara Croft, big time (and increasingly so as the series goes on). Between the first and third games, Lara goes from killing endangered species (though they do attack her) and human enemies with a "saving the world" licence to killing MPs, security guards, homeless and tribesmen in their own village with the flimsy excuse that she's looking for an artefact. Taken to its limit by the sixth game, where she kills dozens of policemen and security guards, breaks into the Louvre and contaminates evidence in two separate crime scenes. All to clear her name of a single murder.
Robot Chicken parodies this quite well. With a sketch showing Lara entering a tomb, in which the monsters inside are extremely friendly and are all too willing to politely hand over their treasures. Regardless she shoots everything she sees to oblivion without saying a word.
In Star Trek Online's Delta Rising expansion, the Kobali are introduced as a peaceful race under attack by a race of brutal conquerors, the Vaadwaur. They quickly prove untrustworthy, however, repeatedly lying to the player about mission-critical information. Also, their method of reproduction, what amounts to necromancy, has drawn a lot of rape comparisons on STO's forums, and they have a habit of forcibly retrieving anybody who remembers their previous life and tries to leave. All the while acting Holier Than Thou like the Federation on a bad day (see the main franchise entry in Live-Action TV). As a couple posters put it, they demand respect for their own culture but offer none in return. In comparison, discounting their leader Gaul, The Heavy of the story arc, the Vaadwaur as a whole are really just your standard Space Nazis (they've drawn many comparisons to the Klingons and TNG-era Romulans and Cardassians, all of whom the Federation managed to have a detente with) and their primary grievance with the Kobali is that the latter are holding thousands of Vaadwaur Popsicles and using the failed tubes, along with Vaadwaur battlefield casualties, for reproductive stock.
Monkey Island: Guybrush Threepwood. is a wacky (sometimes moronic) goofball. His actions have screwed over countless NPCs throughout the series. In the second game, he nails a salesman in a coffin (Who doesn't get out until 3 months later) just to steal a key, frames an innocent woman for countless crimes (Which were all his to begin with) just to steal her non-alcoholic grog, and steals Wally's monocle, in which listening to Wally while he tries to look for it is just heartbreaking. Subverted when he did make amends for them in each case. He didn't mean to nail the coffin down so hard and freed the salesman in the following game, broke the woman out of prison later on, and gave Wally a replacement monocle sometime after that.
The titular Pecan Apple of Banzai Pecan. The game claims she is a paragon of justice and heroism, but her actions in the game can hardly be considered heroic. She threatens the guy she claims to love with denial of sex if he so much as kisses the big bad, gets the hots for another guy who turns out to be her future son, calls them by derogatory names, and acts like a total jerkass to them (some worse than others).
Brent Halligan from The Mystery of the Druids is a mostly ineffective jerkass of a Scotland Yard detective whose time prior to the game's events was spent loafing about, wasting all his money on pizza and gambling, playing practical jokes, and unsuccessfully flirting with his department's data analyst rather than actually trying to solve murder mysteries. As if that didn't already make him unsympathetic enough, his charming actions during the course of the game include robbing a homeless man for change to use a payphone, stealing a French fisherman's expensive rod and bucket just to scrape salt off a ferry, and at the end, stabbing the female lead in the stomach (not without reason, but this was severe overkill just to screw over the villain).
Valdo, the protagonist of Secrets of da Vinci: The Forbidden Manuscript, is an admitted forger and con artist; he lost his previous job for making a copy of a painting and selling it as the original. He also, depending on player choices, has no problems with breaking and entering, lying, theft, and seducing the woman in whose house he's staying. But he's the hero and a major Karma Houdini in the end.
The Persona franchise, while not containing the worst examples of these, have heroes that make you question their actions.
Persona 3: Yukari Takeba reaches this point in The Answer, where she was fully willing to risk The End of the World as We Know It just because she wanted to see the Protagonist again. This only gets worse when Mitsuru, the allegedsmart one of the group, sides with her. Yukari's refusal to listen to reason causes the party to go against each other, and she only really gets a slap on the wrist for her actions.
Persona 4: Despite their desire to seek the truth, the Investigation Team at times act like huge Jerkasses throughout the story. Yosuke often acts like a shameless pervert (right after a girl he had a crush on died, no less) and would often make cracks about Kanji's sexuality, which is something he knows he's deeply insecure about. Chie tends to beat up Yosuke (and on some occasions, the Protagonist and Kanji) regardless of whether he deserved it or not, extorts Yosuke just because he broke a DVD that could have easily been replaced ten times over, and even uses Yosuke's money that he was saving for a motorcycle to buy Teddie an expensive suit (Teddie only gets excused because he was new to the human world and very likely didn't understand how money worked) and then got defensive when she got called on it before Yosuke caved in. The rest of the Investigation Team aren't as bad as Yosuke and Chie, but they have their moments, such as the Protagonist and Kanji coercing the girls into entering a beauty pageant, the girls' actions during the Amagi Inn scene, the moments where they'll mock Hanako and Kashiwagi for their lack of beauty, and the various moments where the victims got kidnapped by their own stupidity.
Persona 5: The Phantom Thieves are a complicated example. Their course of action when dealing with their Targets is basically brainwashing. They occasionally get called on it, but the people that do are usually either antagonists or have their minds changed in the end. The Thieves themselves question their actions, but only rarely. The only other mitigation is that the people they brainwash are Asshole Victims, including an implied rapist, a few murderers, and a Yakuza boss.
Both Dante and Virgil of the Dm C Devil May Cry. Dante is portrayed as a Jerkass who is more interested in having sex and killing demons than helping out humanity. Virgil treats humans like lesser animals, remorseless shot Lilith and her child when she was completely defenseless, and planned to enslave humanity after Mundus is disposed.
The Railroad of Fallout 4 are a loose group of operatives, scientists and idealistic Wastelanders working together to ensure the liberation of Institute Synths, but their noble goal comes with a massive case of Moral Myopia as they entirely dedicate their efforts to helping Synths when frankly everybody in the Commonwealth can use a hand - their best operative, Deacon, laments that even from a purely pragmatic standpoint, it denies the Railroad valuable resources and favours it could be owed in return and makes preaching their message of human/synth co-existence all the harder as few Wastelanders have any reason to trust them. Not to mention how extreme they can be in dealing with their enemies, as whether they're aware of it or not the Brotherhood's Cool Airship, the Prydwen has children aboard, and your final mission with them has you sneaking aboard and rigging it to explode, plus Railroad NPCs will fire upon Institute heavies, scientists and civilians with equal aplomb. What makes it particularly noteworthy of their behavior is that all of the members of the Railroad seem to have unquestionable faith in your decisions.
Though you'll have a tough time fining any faction in The Fallout Wasteland completely good (Besides maybe the Minute Men, also from 4), The Brotherhood Of Steel has been undeservedly portrayed as anti heroes at best, and Lawful Neutral at worst for most of the franchise. Particularly ' 'Fallout 3. They're portrayed this way because they fight the designated villains of The Enclave, they have less genocide, slavery, or all around outright evil behavior in their history than most evil factions, and they give the player lots of cool toys to play with. But they believe that technology and knowledge led to The Great War, and that they're the only ones responsible enough to wield any prewar tech. So they take anything more advanced that a standard firearm, regardless of if it has any offensive capabilities, and rather than use it to save lives or rebuild civilization, they hoard it all to themselves, to be used to sustain their own or to collect more tech, if they use it at all. And if they have to whack a few wasteland civilians or NCR (one of the better factions) soldiers to get the tech, their leadership couldn't care less. Fallout 4 made attempts to rectify this, though, showing that it was due to their different leadership on the east coast that they acted the way they did in 3, and a more traditionalist elder leading in Boston was all they needed to become Jerkasses seeking to slaughter every Super Mutant, Synth, and Ghoul in the wasteland, and the game makes few excuses for it. Luckily, unlike the Railroad, which every member seems to have unquestionable faith in, members of the Brotherhood call out some of the racist attitudes, and one particular mission is about essentially going against orders in front of the commanding officer, which clearly he doesn't even know how to handle the situation given what he feels and what he's told to do. In short, the Brotherhood are definitely treated as one of the 'good guy' factions despite their bad attitude towards others, but at the very least they're not full of people who never question the ethics of blowing up a blimp with children onboard.
Pick a protagonist from the Whack Your... series. Any of them. Though arguably justified, since the whole series runs on Catharsis Factor for those frustrated with their jobs, their teachers, or their computers.
Chin from Hong Kong '97. After "crime rate skyrockeded" [sic] when people from China moved to Hong Kong, apparently the best solution the government could come up with is hire Bruce Lee's relative to single-handedly wipe out China's entire population. Likely including children, since it matches up with the "1.2 billion" goal the game gives. The game still treats him as some kind of hero for this.