It's often said that winners are the ones who write history. That those who prevail in a conflict are the ones who determine how that conflict is perceived going forward. That's not entirely true, though; the winners aren't always the ones who write history. Sometimes, it's the ones with better PR departments.
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Oftentimes in games, protagonist characters, ostensibly heroes, are branded as criminals, monsters, or general malcontents. This can be due to a widespread misunderstanding, like being in the wrong place at the wrong time, but more often than not, it's due to deliberate misinformation circulated by antagonists or bad actors.
9 Link - The Legend Of Zelda: A Link To The Past
It's hard to believe that any iteration of Link could be anything but a universally-beloved hero, but in The Legend Of Zelda: A Link to the Past, he actually ended up as a bit of a social pariah. After he rescues Princess Zelda from the dungeon at the start of the game, Link has her go into hiding with a local priest. The problem with that is that Agahnim, the sorcerer responsible for locking her up, is a widely-respected figure around Hyrule with most of its guardsmen on his payroll.
All it took was one word from Agahnim, and Link is public enemy number one, with many of the residents of Kakariko Village calling for guards upon seeing him. As far as anyone knows, Link is the villain who has spirited away their princess and threatens the stability of the kingdom.
8 Joker - Persona 5
When in character as the leader of the Phantom Thieves, Joker is a charismatic rogue, stealing hearts in both the literal and metaphorical senses. Outside of that, however, he's just a normal high schooler, and for most of his time at Shujin Academy, he's one of the most reviled students around.
Due to Kamoshida leaking his criminal record, most of the students at the school absolutely refuse to associate with Joker, with rumors circulating that he carries a knife, threatens people, does drugs, and other assorted exaggerations. Technically, two of those are true, but his knife is fake, and he only threatens Shadows.
7 Yuri Lowell - Tales Of Vesperia
As a vagabond from the Lower Quarter of Zaphias, Yuri has a great rapport with his friends and neighbors... and that's about it. Due to his standing in society, no one in the upper quarter wants anything to do with him, and due to the misunderstanding surrounding his departure from the capital with Estelle, he's branded a criminal elsewhere.
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In fairness, Yuri has engaged in some extremely shady behaviors, up to and including the murder of a high-ranking Royal Guard, but all of these actions were in the name of the greater good. After all, that Royal Guard was engaged in slavery and human trafficking, something the world could certainly use less of.
6 Booker DeWitt - BioShock Infinite
As part of his indoctrination efforts to maintain control of Columbia, Zachary Comstock instills in its populace a stern warning: a False Shepherd with an "AD" brand on his hand will cause the downfall of the city and its people. This is immediately problematic for Booker DeWitt's infiltration of the flying city since he has that exact brand on his hand.
Booker originally intended to liberate Elizabeth and scram with minimal conflict, but due to the zealotry of Columbia's law enforcement, they never stop pursuing him, not realizing the fact that they are themselves contributing to their city's downfall. This continues to be a problem when Booker is faced by the Vox Populi, as he's branded an imposter of an alternate Booker that martyred himself for their cause.
5 Chuck Greene - Dead Rising 2
Chuck Greene is a pretty quiet guy, only coming to Fortune City to participate in Terror is Reality so he can get some cash to buy Zombrex for his daughter. Unfortunately, quiet, private guys like him make great patsies for unsavory individuals.
Tyrone King and his thugs, at Phenotrans' behest, frame Chuck for bombing the gate to the local zombie pen and causing a fresh outbreak. It's only thanks to Stacey Forsythe's intervention that Chuck and Katey aren't booted from the shelter by Sullivan, and the whole time he's there, the occupants of the shelter are giving Chuck sideways looks.
4 Vault Hunters - Borderlands Series
While not exactly heroes per se, the various Vault Hunters of the Borderlands games, particularly the first two games, aren't bad people. They're just treasure hunters looking to strike it big, occasionally righting wrongs here and there in the process should doing so prove profitable.
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That doesn't stop powerful entities like the Crimson Lance and Handsome Jack from painting all Vault Hunters as violent, world-ending bandits. Handsome Jack in particular has Hyperion's entire PR department cooking up nonsense stories about the horrible things Vault Hunters do, such as the wanton destruction of private property and the slaughter of cute animals.
3 AVALANCHE - Final Fantasy 7
The Shinra Electric Power Company is one of the de facto governing bodies of the entire world of Final Fantasy 7, supplying the city of Midgar with vital Mako energy and supporting its way of life. AVALANCHE, meanwhile, is a terrorist organization that seeks nothing but chaos and destruction. Or at least, that's what the Shinra press release says.
While AVALANCHE is technically a terrorist group, their only goal is the destruction of the Mako reactors before they suck the planet completely dry of its lifeblood. The fact that people lose their power is just an unfortunate byproduct of that.
2 Dante - DmC: Devil May Cry
In the prime Devil May Cry timeline, Dante isn't much of a public figure by design. You need a password to even call Devil May Cry, after all; he doesn't like to make himself known. In DmC, however, the alternate Dante is a bit more... publicly overt, let's say.
Due to smear campaigns by demons and demon sympathizers, Dante is painted by the public as a mass murderer and terrorist with a screw loose. Of course, none of the regular populace realizes that they're firmly under Mundus' thumb and are believing only what he wants them to believe.
1 Michael Wilson - Metal Wolf Chaos
After United States Vice President Richard Hawk stages a military coup d'état, President Michael Wilson is forced to flee the White House aboard Air Force One. As a staunch believer in justice, Wilson takes up the advanced mech suit Metal Wolf to fight back the coup forces and reclaim the country.
However, in order to cement his rule, Hawk makes a press release that Michael was killed, and identifies the Metal Wolf mech as a third-party terrorist. The American populace doesn't realize that the mech skirmishing with the military in the streets is actually their President, fighting for their freedom.
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