Ezio Auditore in his trilogy is a story how he moves from this trope all the way up to Big Good as well.
Connor in Assassin's Creed III is a tragic desconstruction of this trope: he embarks on his quest to save his tribe and avenge his mother who was killed by a fire started by the Templars, and ends up sympathizing with the Colonists' side in the Revolution. However, it turns out nothing as simple as his world views presumed and as he succeeds in killing all his opponents, he fails to protect his people and ends up having to kill his father Haytham when he tried to murder him. And oh, it was the Colonists who gave the order to attack his tribe and not the Templars, meaning he has been assisting the side that ends up driving them away.
Alexios or Kassandra in Assassin's Creed: Odyssey can be played as straightforward heroes at the player's discretion by assisting others free of charge, be kind as helpful as they can and opposing the Cult of Kosmos.
Yugo from Bloody Roar goes from investigating the mysterious circumstances to his father's death to leading a resistance against a corrupt corporation trying to exploit zoanthropes and aims to make a bright future of co-existence between humans and his people.
Crono from Chrono Trigger. While initially he sets to rescue his newfound friend (and potentially Love Interest Marle) from being absorbed by a time gate, he ends up embarking in a quest across time and space in order to avert a Bad Future which happens centuries long after he's dead. All while he saves a Queen from the Middle Ages, defeats a fiend Overlord (which can fight side-by-side with), and a race of reptilians form the Prehistory. In a highly unusual development, he dies about 2/3 of the way through the game, and his revival is an optional sidequest.
Discussed as well, as anyone bearing the "Hero's Medal" is believed to end the war between humans and Fiends, wielding the Masamune. Unfortunately, the first known bearer is killed, the second one is too young and cowardly, and the third is too shell-shocked to ever accept the responsibility (though he can eventually move past his grief and join and help Crono defeat the Fiendlord).
Monica from Dark Chronicle, in one of the few cases where the main protagonist is not also the Hero.
Darkstalkers is a bit complicated about it: Demitri Maximoff was supposed to be the actual protagonist of the series, until Morrigan Aensland took over his place, but neither of them fit the traditional heroic archetype since they are morally ambiguous of varying degrees and motivated by power and hedonism, respectively. Donovan Baine is the closest one to qualify due to being motivated to hunt evil monsters and he is the one to confront Pyron in the OVA.
Although there's the possibility of it being too obvious to be worth listing here, the majority of the main characters in every Dragon Quest game serve as the Hero, to the point that in Dragon Quest VIII the hero's default name is Hero. Nearly all of them have balanced abilities and use (or have the option of using) swords, and many of them have lightning and/or fire in their selection of attack magic.
One of the only exceptions is the Hero from Dragon Quest II, who learns no magic at all and serves as the physical fighter of the party.
In Dragon Quest I, the Hero was born and bred for the job in a world where the Dracolord had already won.
Similarly, the hero of Dragon Quest III was trained since childhood to save the world and avenge his father by destroying the evil Baramos.
In Dragon Quest V, the trueLegendary Hero destined to defeat Grandmaster Nimzo turns out to be The Hero's son, making him and his mother the only members of the party with any relevance to the prophecy.
Daggerfall: The Agent, a personal acquaintance of Emperor Uriel Septim VII sent to the eponymous city to investigate the death of its King, who quickly becomes embroiled in a plot to reactivate a Lost Superweapon that will forever shape Tamriel. (Literally, as the case may be.)
The Civil War questline is nearly as expansive as the main quest, and has the Dragonborn work with either the Empire or the Stormcloak rebels as essentially a One-Man Army to claim Skyrim for one side or the other.
Dawnguard follows the Dragonborn who can choose to work with the eponymous Vampire Hunter organization against a powerful group of vampires who seek to invoke a prophesy to bring about The Night That Never Ends, or work against the order as one of the vampires.
Dragonborn has the Dragonborn visit Solstheim, where he/she comes into conflict with Miraak, the first Dragonborn who seeks to return.
In the Fable series, Heroes are a classification of people in Albion who possess the disciplines of Strength, Skill, or Will, and as such have extraordinary fighting and magical abilities. The player character in each game has control over all three disciplines, and can either play this trope straight or horribly invert it.
Played straight in most of Fallout 3, but subverted in four of the five add-ons (Broken Steel being a continuation of the main storyline, very heroic, and something of an Author's Saving Throw for the original ending). The main game revolves around one man's dream to bring free, radiation-free water to the Wasteland, and how his child either achieves or subverts that dream.
Operation Anchorage requires the player to aid one of the least sympathetic non-psychopathic factions in the game (who only exist as a faction because they broke away from a group that decided it was more important to protect innocents from 8-foot-tall genocidal mutants than to hoard technology).
The Pitt forces the player to choose between allowing miserable slavery to continue in the name of rebuilding the only working steel mill on the east coast and finding a cure one of the most devastating mutations in the Wasteland, or freeing the slaves by replacing a Reasonable Authority Figure with his treacherous lieutenant, who then plans to use his former Lord's infant child to find a cure as fast as possible, her health be damned. Also, it is implied that choosing the latter will allow the steel mill to rot, a significant setback for rebuilding.
Point Lookout has the Lone Wanderer caught between a badass and a Chessmaster. While none of their actions are decidedly heroic or villainous, they get outsmarted by brain-damaged drug addicts and (depending on what side quests they follow), a 200-year-old death trap. Both these events paint the hero as more of a gullible incompetent than anything else.
Mothership Zeta is mostly a fight for survival, ending with the player willingly destroying a craft capable of traveling to other planets. That, you know, aren't ruined.
Tidus from Final Fantasy X is clearly the main character to the player, but he's a late-comer to the other characters, who already composed the rest of The Team before he showed up.
Yuna takes up this role in the sequel. Very interesting considering that she was The Chick in the previous game. She even fights like Tidus and uses one of his swords in her Warrior dressphere.
Though Alm and Celica share the role of main protagonist in Fire Emblem Gaiden, Alm is probably the better fit for this specific trope, being the dashing leader of the Deliverance resistance group.
Sigurd of Fire Emblem: Genealogy of the Holy War is a deconstruction of this. He's a mighty warrior with a kind heart and a strong sense of honor, but his naivete and black-and-white worldview leads to him becoming a disposable pawn who inadvertently helps create a tyrannical empire. Fortunately for everyone, his son Seliph is a Reconstruction who's able to succeed where his father failed.
Leif of Fire Emblem: Thracia 776 is a kindhearted young man who eventually develops the maturity to be the leader the northern Thracian resistance needs.
While Chrom is the leader of the Shepherds in Fire Emblem Awakening, with his charisma and idealism being vital to their success, player avatar Robin is not only the group's tactician, but a mighty and versatile warrior who's the only character capable of befriending every Shepherd.
There is also a character class called "Hero," but that's a bit of a misnomer as they're simply the promotion of the Mercenary and/or Fighter class.
The Five Nights at Freddy's series has the various night guards throughout the series who in the Freddy Files and Survival Logbook, are all hinted to be Michael Afton. As well, there is the Crying Child from Five Nights at Freddy's 4, who is the protagonist of the 8-bit minigames and maybe the main gameplay. Or it could be the older brother. We aren't sure. And the older brother could be Michael.
Glory of Heracles III plays with this by having two nameless Amnesiac Heroes whom the player names, the first party member and the final party member, with the two referred to as "the Hero" and "the Protagonist." There's a very good reason why the main character isn't "the Hero."
From Halo, Master Chief Petty Officer John-117 of the Spartan-IIs. Not the strongest, fastest, smartest of the Spartans, or the best at any category at all, except in leading the others and always getting the job done. He is so unbelievably Mario in comparison that even though there is at least one Spartan that can do something better than him, he wins everything because there is nothing he is bad at. Nothing. And he knows it. That's why he was made The Leader of the rest. Although Cortana says he has one thing the rest didn't: LUCK.
Another thing he is the best at is being the Bravest with a capital B, as said by Dr. Halsey herself. Spartans are by definition extremely brave and invulnerable (latter mostly as symbolism, but also proven with them having the best survival rate per engagement). However John takes it to the pure insane, combining it with his luck and courage to do the pure impossible even by Spartan standards.
Black Orchid in Killer Instinct is considered the main protagonist of the series due to having appeared in every game and being the canonical victor, though she arguably shares the role with her brother Jago.
In Kingdom Hearts: Birth by Sleep, Aqua is by far the hero. She is the only one to achieve the rank of Keyblade Master, never succumbs to darkness, puts her friends above herself, and always fights to help others above all else.
From the Mother series, we have Ninten, Ness, and Lucas, although it takes Lucas a bit of time before he becomes the hero of his game.
Octopath Traveler: Each of the main characters is heroic and selfless. However, a few Ophilia and Olberic, in particular are more genuine traditional heroes, whereas characters like Therion and Primrose are more of an Anti-Hero, willing to break the law and/or kill people if the situation requires it.
Rosalyn from Okage: Shadow King is another case of the hero not being the player character, generally being a superb Hero's Guild Member and overshadowing Ari. But then, everyone does that last bit.
Devlin McCormack from The Orion Conspiracy. Unlike a lot of games out there, he is different. How so? For starters, he is a middle-aged guy who has a number of issues. He was not a good father or a good husband. He does feel bad about it. His son and wife are both dead. He fought as a soldier in the Corporation War. However, the game demonstrates that he seems to prefer using his brains and guile rather than a gun and physical combat. He also engages in lying, petty larceny, blackmail and some Shoot the Dog moments. The Chick is also not attracted to him. With all that said, he does lead the charge more than once in the game.
Prince of Persia: The titular nameless prince in nearly all the games except Prince of Persia: Warrior Within and Prince of Persia (2008) where he is more of an Anti-Hero where he is fighting for his own self-preservation in the former and is a thief and grave robber in the latter. In all other games though, he is more traditionally heroic trying to save the princess from some evil vizier or a terrible sand monster unleashed upon the land.
Quest for Glory: Unsurprisingly, the main protagonist titled as the Hero (though his canon name is Devon Aidendale) is this trope by profession. Though he can pursue any class from Fighter, Mage, Thief and The Paladin, the whole series is about becoming more virtuous and heroic as it progresses.
In Sly Cooper, Sly is the hero even though he's a thief. Even though he's considered a criminal because he steals, he only steals to save the world from criminals who actually are evil and have devious intentions.
Soul Series: Sophitia was canonically the one who defeated Cervantes and destroyed Soul Edge at the end of the first Soul game. Later games would put Sophitia as a supporting character in favour of Xianghua (Calibur), Siegfried (Calibur II, III and IV), Sophitia's sonPatroklos (Calibur V), and now Kilik (Calibur VI). Sophitia however has the most in common with traditional fighting game heroes, being the balanced, newbie-friendly character.
Deconstructed hard in Spec Ops: The Line. Captain Walker's desire to be a hero is what causes him to kill American soldiers, drop white phosphorous on innocent civilians and generally sentence every person in Dubai to certain death.
Fox McCloud of Star Fox. The Leader of the titular mercenary group and The Ace pilot, he carries the legacy of his deceased father and ace pilot, James McCloud, in order to defeat the galactic emperor Andross, and then stopping the Aparoids and the Anglars.
Guile also fits this trope. He is the one who consistently takes on Shadaloo, and is arguably one of Bison's greatest adversaries.
Rashid from Street Fighter V also qualifies. While Ryu delivers the final blow on Bison, Rashid is ultimately the guy who saves the day by stopping Bison's doomsday machine. Rashid also has more storyline fights than anybody else and he is the character given the most screentime, by far.
The Legend of Heroes: Trails in the Sky First Chapter and Second Chapter has Estelle Bright as the main protagonist of the game and the heroine of the story, who starts off her adventures as a bracer.
The Legend of Heroes: Trails in the Sky The Third has Kevin Graham who was a party member in SC and ends up being the hero of his own game as he struggles with his mistakes and failures, and learns to accept them.
Vampires Dawn: Valnar is the main protagonist and will fit this trope like a glove if played Friendly Neighborhood Vampire. At least the second game assumes you played it this way, given it starts with one ending where you were a good guy.