Entries in each group are by release date.
- (The Amazing) Spider-Man vs. the Kingpin (Sega CD version): Wilson "The Kingpin" Fisk frames Spider-Man for the theft and intended use of a nuclear bomb, which he himself intends to use to destroy New York City as part of a plan to Take Over the World and rid himself of Spider-Man once and for all; if the player runs out of time, the bomb goes off and destroys New York just as he planned. He additionally frames Spider-Man for kidnapping and threatening to kill Mary Jane, part of a plan to lure him to his hideout for the final showdown. Should Spider-Man fail to save Mary Jane from acid in time, the Kingpin laughs and mockingly offers condolences, and if he gets defeated by Kingpin, the latter kills them both onscreen, savoring every moment. Lacking any of his comic counterpart's nobler traits, this Kingpin is willing to do anything and everything to destroy Spider-Man and New York itself.
- Spider-Man 3 (PS3, 360, PC version): Luke Carlyle is a former industrialist whose business crumbled after the Daily Bugle uncovered his corrupt practices. Seeking revenge against the city that ruined him, Carlyle adopted the identity of "Carlyle the Mad Bomber" and led a series of terrorist attacks across Manhattan. After destroying his old building, Carlyle had his men plant explosives throughout the city, focusing mostly on locations that would cause civilian casualties. When Spider-Man foils his plans, Carlyle launches an attack on the Daily Bugle and kidnaps J. Jonah Jameson. Carlyle places an explosive collar around Jameson's neck and tosses him out of his helicopter in an attempt to kill him and Spider-Man. Carlyle ultimately escapes after Spider-Man takes out his helicopter, but not before setting off the explosives he had rigged in each of his henchmen's suits.
- Web of Shadows-Amazing Allies (PS2 and PSP) Edition: Venom, Eddie Brock, is the main antagonist of this alternate telling of the story, and is nothing like any of his other incarnations. Hating Spider-Man for untold reasons, Venom allows Jackal to experiment on him in order to speed up his symbiote suit's growth rate, then spreads his symbiote across Manhattan, infecting hundreds of people, including Spider-Man's friends, and turning them into mindless, hate-filled zombies. After manipulating many of Spider-Man's foes into assisting him in destroying the Wall-Crawler, Venom reveals he plans to allow his symbiote to spread across the planet, infecting every human around the world once Spider-Man is dead.
- Shattered Dimensions: Mysterio—Quentin Beck—is portrayed as far more wicked and dangerous than in the comic. Failing to steal the Tablet of Order and Chaos due to Spider-Man's interference, Mysterio escapes with one of the now-shattered fragments of the Tablet. Realizing the power of his fragment, Mysterio goes on a rampage, destroying anything in his path. After finding Madame Web's location, Mysterio tortures her, then uses her as a hostage to force Spider-Man to retrieve the rest of the Tablet's fragments for him. Restoring the Tablet to its original state, Mysterio gains god-like powers, destroys the Multiverse, and plans to remake it in his image.
- Marvel's Spider-Man: The City that Never Sleeps: Hammerhead is a sadistic Maggia don who yearns for the "good old days" where mobsters like him ruled New York City with an iron fist, and the police knew to look the other way. When Sable International leaves their technology behind after the Devil's Breath incident, Hammerhead arms his men with as much as he can find and tears up the streets of New York with a brutal gang war against the other crime families so he can seize power from them, attempting to have numerous civilians killed. When Spider-Man and his cop ally Yuri Watanabe attempt to stop him, he provokes Yuri into shooting him by killing numerous cops while stealing the dangerous Project Olympus armor before having other crime bosses slowly drowned in cement, trying to broadcast their deaths across the city. When that fails, he goes into hiding and has himself converted into a cyborg, forcing an Oscorp scientist into upgrading his men with cybernetic enhancement, not caring that some of his men would die due to the procedure. When he resurfaces, he tortures Silver Sable with a power drill until she gives him the most dangerous Sable Tech in her arsenal.
- Next Dimension: Bastion is an AI who claims to defend humanity against mutants but is really just a psychopath. After being freed from SHIELD captivity by his Prime Sentinel minions, Bastion devises a new scheme to destroy mutantkind. Bastion hires the Brotherhood to attack Xavier's school and uses that attack as a distraction so his Sentinels can kidnap Forge, a mutant who can invent anything. Bastion proceeds to torture Forge, forcing him to build a device that neutralizes mutant powers and then outfits all of his Sentinels with that device. Bastion ultimately plans to use this device to depower the world's mutant population, so that he can easily kill them off. Though Bastion claims he is guided by good intentions, he is really just a sadistic bigot.
- X2: Wolverine's Revenge: The Professor, real name Truett Hudson, is a mastermind behind the Weapon X project, an experiment designed to create the perfect killing machine. To this end, the Professor experiments on a least a dozen people, turning them into mindless feral mutants, before he gets his hands on Victor Creed, aka Sabretooth, and Logan, aka Wolverine. Kidnapping the two, the Professor commits a number of painful experiments on them, wiping their minds and turning them into perfect soldiers. When Logan escapes and confronts the Professor, the latter informs him that he injected all Weapon X subjects with the Shiva Virus, which would kill them in a few years, leading to Logan starting to search for the cure several years later
- Legends II: Rise of Apocalypse: Apocalypse is once again presented as a extremely cruel Social Darwinist. Apocalypse starts the game by conquering Genosha, locking all the Genoshan mutants in a makeshift prison so he can test them for harmonic DNA, a particular DNA type that will increase his own power. When the X-Men come to liberate Genohsa, Apocalypse attempts to destroy the Genoshan Sea Wall, which would have killed almost every mutant in Genosha. After Genosha is liberated, the X-Men track Apocalypse's forces to the Savage Land, where they attempt to destroy the technology that keeps the Savage Land in tropic temperatures; this would result in the inhabitants of the Savage Land freezing to death. Later Apocalypse manages to conquer New York City, dropping a bomb that flattens several neighborhoods, just to make room for his tower. Apocalypse again imprisons the mutants and tests them for harmonic DNA, while having his forces attempt to drive the human refugees into the sea, setting up anti-aircraft guns to prevent anyone from rescuing them. Apocalypse is such a powerful and cruel foe that the X-Men and the Brotherhood team up to stop him.
- Destiny: Bastion is an AI created to defend humanity against mutants, but grew beyond his programming and became a threat to humanity. Seemingly killed in battle with the X-Men, Bastion survives by uploading his program into an orbiting satellite. Making contact with Luis Reyes, the head of the Mutant Response Division, Bastion creates a plan to take over the world by turning everyone into his mindless slaves. Directing Reyes to obtains a sample of Xavier's DNA and uses it to replicate Xavier's Psychic Powers, so that he can take control of the MRD, U-Men and the Purifiers, Bastion has him kidnap mutants and subject them to dangerous and potentially lethal experiments in order to harvest more mutant powers. Bastion then orders Reyes to cause further tension between humans and mutants in San Francisco by launching an attack on a rally which was supposed to promote peace between humans and mutants, and framing Magneto.
Marvel Cinematic Universe non-canon tie-in games
- The Incredible Hulk (2008 Video Game): Major Glenn Talbot, a far cry from his later MCU characterization, is a homicidal army major obsessed with taking down the Hulk, Bruce Banner, through any means necessary. Beginning his attacks on Hulk by launching numerous missile strikes on him, Talbot disregards his soldiers' objections that the missiles will impact many highly-populated areas of New York, and pins all the ensuing destruction on the Hulk. When press helicopters fly too close to his military base, Talbot orders them all shot down, hoping to silence the reporters' attempts to oust him as a madman. Showing no care for innocents, Talbot kidnaps both Hulk's best friend, Rick Jones, and his Love Interest, Betty Ross, to use as hostages to draw him out, and, when the army turns on him after they learn of his crimes, Talbot responds by killing the soldiers sent after him, attempting to murder the Hulk, then setting his Hulkbuster armor to detonate, fully knowing it will wipe out most of the city, just to kill the Hulk. A sociopath who abused his power for no reason other than blind hatred and jealousy, Glenn Talbot stood out, even to Bruce Banner, as a truly wicked man whose hatred made him far worse than the "monsters" he claimed to be fighting.
- Thor: The Dark World: The Official Game: Malekith the Accursed, the leader of the Dark Elves and the root of all evil in the game, differs from the version seen in the film. Desiring to return the universe to the "darkness" that existed before life sprouted throughout the cosmos, Malekith begins collecting powerful Uru weapons to use in a ritual to fulfill his desire. Sending his minions throughout the Nine Realms, Malekith has innocents killed, monstrous creatures released, and entire villages razed to the ground, all in various attempts to distract Thor from stopping him. With no loyalty to his "partners", as seen when he betrayed and attempted to murder both the Frost Giants and the God of Mischief, Loki, when they outlived their usefulness, Malekith proclaims himself a god before trying to wipe out all life in the universe, so as to make the Dark Elves the reigning power once again, with himself as ruler supreme.
- Future Fight: M.O.D.O.K. is revealed to be the instigator of the collapse of reality in this game. He sends Jocasta into the past to distract the Avengers from his plans to destroy the universe and remake it in his image by having Jocasta distract the Avengers from exposing MODOK's goals by making them focus by other villains such as Ultron, HYDRA and Fisk. This in turn leaves the Avengers with no time to stop reality from destroying itself. When the Avengers defeat their Bad Future counterparts in Chapter 8, MODOK reveals that he was responsible for sending Jocasta to the past to prevent the Avengers from stopping him, having done this 90,000 times in the past before, with each effort having the same outcome in facilitating the destruction of reality, with every reality being more unstable than the last. He subsequently orders Jocasta to reset the timeline, leaving the Avengers to their fate while he recreates the universe in his own image.
- The Punisher: General Kreigkopf is the leader of the Russian Syndicate in the second portion of the game. An associate of the Gnucci Family, Kreigkopf would supply them with drugs and money from the harbor. When Castle attacks the harbor, he discovers Kreigkopf has been smuggling in weapons, including a tank and a nuke. Frank discovers that Kreigkopf is also part of a Human Trafficking ring. Kreigkopf sends the Russian to attack Castle at his apartment. When Castle and Furry invade Grand Nixon Island, he prepares to launch the nuke at New York City, and manages to get it to the point it's supposedly irreversible before Frank kills him.
- Ghost Rider (GBA version): Mephisto is behind all the evil in the game. Seeking to expand his hellish kingdom, Mephisto decides to create a Hell on Earth by drawing a glyph that would break the seal between Hell and Earth and trigger the apocalypse. Choosing Johnny Blaze to become the Ghost Rider, he has his dad killed, and orders Vengeance to kill his girlfriend Roxanne when Blaze refuses to serve him. Once the glyph has been drawn into the Earth by Johnny, Mephisto tries to kill Johnny so that nobody can stop him.
- Marvel vs. Capcom: Infinite: Ultron, upon fusing with Sigma, begins seeking the Infinity Stones to remake both the Marvel and Capcom universes to his liking. Attacking Xgard, Ultron Sigma uses the Sigma Virus to enslave its people, parading them in front of Thor before infecting him and forcing him to fight his friends while Ultron gloats. He also schemes with Grandmaster Meio to drop a bomb on Earth to infect all living things on the planet. When Dante tricks him with the Soul Stone, Ultron Omega attempts to slowly drain him of his life. Desiring nothing less than the extinction of all souls, Ultron is loathed by every hero and almost every villain.