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- Akuma: Akuma is the brother of Ken and Ryu's master. He has pushed his fighting skills beyond a normal person's, and seeks to battle only the strongest that the world has to offer.
- C. Viper: Crimson Viper is a deep cover C.I.A. agent posing as a scientist for S.I.N. Her uniform conciles deadly weapons that she uses in battle.
- Cammy: Cammy appears to be a young girl who serves and obeys the commands of her superior M. Bison. She assisinates any target she is ordered to with deadly precision.
- Charlie: Charlie is a first lieutenant in the United States Air Force. He is assigned the task to investigate M. Bison and take down his organization. He will be captured and experimented upon by Shadowloo.
- Chun-Li: Chun-Li is an Interpol agent. She is investigating information about an underground crime lord named M. Bison who she suspects killed her father.
- Dan Hibiki: Dan is a terrible fighter who seeks to become a champion all the same. He uses a flawed form of attack that is otherwise similar to Ken and Ryu's.
- Dhalsim: Dhalsim is an Indian mystic who fights only to restore the balance between good and evil.
- Guile: Guile is detemined to find out if the rumors are true about his best friend and commander, and learn if Charlie was really turned into a killing machine by Shadowloo.
- Ken: Ken is the friend and rival of Ryu. He focuses on flashy attacks designed to wow his opponents. He longs for a rematch with his former training partner.
- M. Bison: M. Bison is the leader of a new underground crime organization, Shadowloo. He seeks to populate his army with the most powerful fighters in the world, enhanced with the aid of his own Psycho Power.
- Ryu: Ryu is a young devoted martial artist who seeks to become the greatest fighter in the world.
- Sakura: Sakura is a young school girl who becomes obsessed with fighting after she witnesses Ryu beat up some criminals. She seeks to ask Ryu to teach her to become a better fighter. She has been seen with an extended tan which seems to alter her abilities.
- Zangief: Zangief is a great wrestler from Russia who is out to prove to the world that Russia is home to the greatest fighter in the world. He discovers a robot version of himself made by Shadowloo known only as Mech Zangief, and mysteriously gains the ability to turn into it.
- Anakaris: Anakaris is the enchanted mummy of one of the greatest Pharaohs that ever ruled Egypt. And he is determined to prove his power and rule it once more.
- Anita: Anita (from the Darkstalkers series) appears as a hidden character in the Japanese version of Marvel Super Heroes. She also uses the sword of Donovan in her attacks.
- B.B. Hood: Baby Bonnie Hood is a twisted little girl who happens to be quite gifted in the art of hunting down and killing Dakrstalkers. Don't let her cute demeanor fool you and watch out for all the heat that she packs under her cloak.
- Felicia: Felicia is a rare cat-woman who is out to prove to the world that not all Darkstalkers exist to harm humanity, and that they can help humans and live side by side.
- Hsien-Ko: Hsien-Ko and her sister, Mei-Ling were normal girls turned into a hopping ghost and talisman to save their mother from death. Hsien-Ko has a massive number of metallic weapons hidden in her sleeves.
- Morrigan: Morrigan is a succubus and the adopted daughter of Belial Aensland. When she was born, Morrigan was extremely powerful, so much so that Belial sealed away part of her power. She lives for the thrill of combat.
- Mega Man: The original Mega Man is the hero of several of his own games. Created by Dr. Light, Mega Man is a courageous robotic boy with powerful blaster at the end of one arm.
- Roll: Thought of as Mega Man's sister, she fights with as much courage and nearly as much power as her brother, for the safety of those that she loves and the world that has embraced her.
- Servbot: One of the 41 tiny robotic constructs that serve Tron Bonne and carry out her various missions has entered the battle on his own, determined to impress his "mother" and make her proud.
- Tron Bonne: Tron Bonne's motives are mysterious. While she has been misunderstood in the past, she is determined to prove that anyone who wishes to mess with her universe has to mess with her first.
- Zero: Created by Dr. Wily, Zero is a violent Maverick turned elite Maverick Hunter and ally to Mega Man X. With his Z-Saber and Z-Buster, Zero protects robots and humans alike from the Maverick menace.
- Albert Wesker: The ex-commanding officer of S.T.A.R.S., Wesker betrayed his team and traded his humanity for power with a virus that made him superhuman strength, speed and regeneration. Now Wesker seeks make the entire world infected with a new virus.
- Chris Redfield: Fresh from the nightmarish experience fighting virus infested zombies in Kijuju, Chris uses his professional training to take down those who threaten the world.
- Jill Valentine: A victim of Wesker's experimentation, former S.T.A.R.S. agent, Jill has a new look but still is able to hold her own against terrorist dealings.
- Amaterasu: The Shinto sun goddess taking on the form of a white wolf, Amaterasu was sealed for one hundred years as a statue, she's revived to deal with evils that have been released.
- Amingo: Amingo is a plant-man on a search for a wind that is sweeping across his land and destroying any plant life that it happens to come into contact with.
- Arthur: Arthur is a valiant knight who fights the undead and various other supernatural creatures to protect his beloved Princess.
- Captain Commando: Captain Commando obtained special ruby shades that allow him to summon his armor. Wherever he goes, the Commando Team is never far behind. The Captain Sword attack assembles his entire team.
- Cyber Akuma: A cyborg, amped up version of Akuma created by Apocalypse. Also serves as the game's final boss. Called Mech Gouki in Japan.
- Dante: A demon-hunting mercenary, Dante has supernatural powers granted from his own half-demon heritage. He uses these powers with his sword and gun fighting skills.
- Hayato Kanzaki: Hayato comes from a dark future where he fights against the evil in his world with his weapon, the plasma sword, which he wields with precision and expertise.
- Jin Saotome: Jin hails from a futuristic era of the Capcom Universe where people pilot giant mechs in combat, but Jin knows several combat moves of his own. His mech is known as Blodia and is featured in some of his attacks.
- Mike Haggar: The mighty mayor of Metro City, Haggar uses his pro-wrestling moves and steel pipe attacks to crush criminals.
- Nathan Spencer:
- Ruby Heart: She is a French-speaking pirate who owns the flying ship that is responsible for carrying the Marvel and Capcom heroes into battle. Ruby Heart is looking for the mysterious orb that the final boss Abyss possesses.
- Strider Hiryu: The Striders are a group of ninja-like secret agents specializing in kidnapping, assassination, demolition and other specific tasks, with Hiryu himself belonging to the "Super A Grade" class. Hiryu's primary weapon is the "Cypher", a plasma-generating broadsword with a tonfa-like handle, although sometimes he is assisted by robotic companions.
- Sonson: The granddaughter of a legendary Capcom hero is set out to make a name for herself and prove that she is just as heroic as her grandfather who once wielded the staff she now possesses.
- Trish: Trish is Dante's ally and fellow mercanary, created by the demon, Mundus. She has powers over electricity and sword and gun skills that rival Dante's.
- Viewtiful Joe: Joe was a fan of superhero movies, until Captain Blue gave him his own V-Watch. Now he's Viewtiful Joe, the superhero protector of Movieland. Joe can slow down, speed up or zoom in the area he's in.
- Cable: The time-transplanted son of two incredibly powerful mutants returns to the present to stop evil… as long as he can control the virus that threatens his life.
- Colossus: Colossus is the slowest, but strongest X-Men member. His attacks involve pummeling the opponent and taking advantage of his metal skin.
- Cyclops: Cyclops is a mutant with the inability to control the optic blasts that emit from his eyes without the aid of special glasses. He has a great amount of agility and an uppercut move.
- Deadpool: Deadpool is.. Ah ah, I got this. I'm the merc with the mouth, I have swords, guns, healing factor, a Dragon Punch and a winning personallity. I mean why not pick me?
- Gambit: Gambit is a cajun with a mysterious past. He has the ability to charge objects up with kinetic energy which explode upon contact. He is also a combat expert with a staff.
- Iceman: Iceman attacks his enemies with ice beams or ice balls. An interesting point is that he takes zero chipping damage when blocking a projectile attack.
- Marrow: Marrow is a young mutant with the power to grow her bones into weapons and remove them to attack, but the most dangerous bone is the chip on her shoulder.
- Phoenix: Phoenix is a mutant psychic, that has the power of the Phoenix Force, with the ability to create "cosmic fire". When endangered she turns into the powerful Dark Phoenix.
- Psylocke: Psylocke, utilizes both Ninjutsu attacks and psionic blasts, with equal ease and speed. She also employs illusions, enabling sneak attacks.
- Rogue: Rogue has the unsual power to absorb abilities from anyone that she makes direct skin-to-skin contact with. She also has enhanced strength and limited flying capability.
- Storm: Storm is the only X-Men member who can fly and mainly attacks with wind and lightning-based attacks.
- Wolverine: Wolverine has moves related to his powerful brawling and clawing skills. He has great agility and can also heal part of his damage.
- X-23: The young female clone of Wolverine, X-23 has claws on her wrists used for various slashing attacks. She is faster and just as agile as Wolverine.
- Captain America: Captain America gained superior strength thanks to an experiemental soldier serum. He uses his shield for most of his attacks.
- Hulk: The Incredible Hulk (Based on the "Professor" persona) is a slow, but powerful character. As expected, his attacks involve the use of gamma energy and strength.
- Iron Man: Iron Man uses energy attacks that include beams and blasts as well as explosives. He can also fly.
- Spider-Man: Spider-Man's attacks are based on his web abilities as well as his great amount of agility.
- She-Hulk: She-Hulk is powerful like her cousin, the Hulk, but is also smaller and more agile than he is.
- Thor: Thor's attacks inclued attacks with his hammer and lightning-based attacks.
- War Machine: War Machine's abilities came from an advanced suit of armor, designed using technology from Stark Industries, and later from an alien-built suit. He is well known as the best friend of Tony Stark, whose Iron Man armor Rhodes has worn on several occasions.
- Apocalypse: Apocalypse is one of the prominent foes of the superhero group the X-Men. He can rearrange the molecules of his body for various purposes. His entire body can be reshaped at will, turning into weaponry, size alteration, and elongating limbs.
- Blackheart: Blackheart is tall and somewhat slow, but he has powerful dark magic and demon-summoning attacks.
- Doctor Doom: Doctor Doom takes great advantage of his armor's abilities and uses magical attacks as well. His armor grants him the ability to do beam and energy attacks. Doom also has the ability to fly with his jetpacks. With these vast amount of abilities, Dr. Doom is arguably as powerful as Thanos, if not more.
- Dormammu: Dormammu is slow, but has many fire-based attacks at his disposal.
- Galactus: Galactus is the devourer of worlds, he is a massive force for the heroes to take on.
- Juggernaut: Juggernaut is slower than the other characters, he usually ignores the first hit of any combo, and his attacks can still devastate the opponent. He can pick up objects from the ground that he can use against enemies.
- Magneto: Magneto is very powerful. He has a great amount of agility, and his attacks are mainly magnetic and energy-based. He can also fly.
- M.O.D.OK.: M.O.D.O.K. can fly and can fire psychic energy blasts from his mind.
- Omega Red: Omega Red mostly makes use of his tentacles, draining either the life- or X-energy or whipping them at the player.
- Onslaught: Onslaught is the nightmarish psychic fusion of Professor Xavier's and Magento's mind, bent on the destruction of the world and all of its saviors.
- Sabretooth: Sabretooth is the sworn rival of Wolverine. Possessing similar enhanced strength and senses to Wolverine, he uses a lot of slashing attacks.
- Sentinel: Sentinel is the largest regular character. He is slow and awkward, but features a vast array of intimidating short- and long-range weaponry, and extremely powerful blows - Sentinel's normal moves inflict guard damage to blocking opponents.
- Shuma-Gorath: Shuma-Gorath mainly uses magic attacks as well as attacks that take advantage of his unique shape. He can also absorb life energy from another character with one of his attacks.
- Silver Samurai: Silver Samurai features an array of Kendo strikes and throwing stars. He can also use his mutant abilities to energize his sword in a vast array of ways.
- Spiral: Spiral uses her long, powerful six arms. She is a great grappler, and can teleport at will.
- Super Skrull: Super Skrull has all the powers of the Fantastic Four. He can stretch his limbs, go invisible and have rock and fire-based attacks.
- Taskmaster: Taskmaster copies attacks from many Marvel heroes including Captain America, Spider-Man, the Black Knight and Hawkeye.
- Thanos: Thanos has a great number of attacks, mostly centered around the gems. While he can use his titanic strength to do normal attacks against opponents, he can use the gems to devastate them. Thanos can perform a supermove for each of the six gems. He also has great agility, which is unusual given his size. However, Thanos is not as powerful as Magneto in the previous game.
- Venom: Venom is the result of the joining of an alien symbiote that once fought with Spider-Man, but was later rejected by him, and a reporter who bore a grudge against Spider-Man.