Marvel: Ultimate Alliance 3 is the third and final installment of the Marvel: Ultimate Alliance trilogy. This also adapts the Secret Invasion storyline.
Deadpool breaks the fourth wall, "Hey fans, I'm just little upset because Marvel Studios are being idiots on holding up on Galactus being the main villain because they want Thor to say he hold him off, but he didn't explain how, and also that good or bad future thing Uatu the Stalker say about not saving either Jean because she might be Dark Phoenix or Nightcrawler because Mystique's gonna kill Professor X to disband the X-Men, and also taking a hard time trying to save Lilandra and not saving her because a meteorite is going to kill the West Coast Avengers, but I did hear that Black Widow could really be a traitor because she framed my little buddy, Weasel into stealing brains scans of Nick Fury, which led to the Civil War sequel where Tinkerer took control of Nick Fury's mind, and I bet he has something to do with Galactus, whoever those Masters of Evil type villains are, they may be up to no good. News flash, I'm calling my buddy, Peter of High Moon Studios to fix this"
- Captain America (Rino Romano)
- Iron Man (John C. McGinley)
- Thor (Jeff Bennett)
- Spider-Man (Jason Marsden)
- Elektra (Veronica Taylor)
- Wolverine (Steven Blum)
- Storm (Candace Putton)
- Deadpool (Drake Bell) - breaks the fourth wall and helps our heroes in finding a villain called, "Main Antagonist", whose gender is unspecific, but Black Widow seems to be working with Antagonist in stealing Fury's brainwaves seeing how his brain scans were violated by microcells, so Antagonist hired Tinkerer to have the Fold take control of Fury's brain to find the Muonic.
- Thing (Clancy Brown)
- Mr. Fantastic (D.B. Sweeny)
- Invisible Woman (Nichole Sullivan)
- Human Torch (Will Friedle)
- Iceman (Will Friedle)
- Daredevil (Ben McKenzie)
- Spider-Woman (Sarah Michelle Geller)
- Black Panther (Kevin Michael Richardson)
- Secret Warriors:
- Nick Fury (Mark Harmon) - investigates Black Widow after realizing she must've given his brain scans to Tinkerer, giving him access to all of the S.H.I.E.L.D. Operations such as the one where they take the Muonic Inducer from Galactus in the Skrull Planet, and Fury had kept the Muonic Inducer in the Vault for inspection.
- Daisy Johnson/Quake (Alison Stoner) - Nick Fury's right hand, and the daughter of Calvin Zabo/Mr. Hyde
- Yo-Yo Rodriguez/Slipknot (Janyce Jaud) - the daughter of John Horton/Griffin
- J.T. Slade/Hellfire (Troy Baker) - a descendent of the Phantom Rider
- Sebastian Druid (Mitchell Whitfield) - son of Dr. Druid
- Eden Fesi/Manifold (Doug Jones) - a mutant
- Jerry Sledge/Stonewall (Ty Olson) - son of Carl Creel/Absorbing Man
- Alexander Aaron/Phobos (Andrew Francis) - son of Ares
- Thanos (Paul Dobson) - main antagonist (a name used by Deadpool) to keep his gender unspecific, but orchestrated Tinkerer having the Fold take control of Nick Fury's brain to steal the Muonic Inducer for a vile plan of, near the end, he was revealed as the secret identity of Main Antagonist, and he reveals his plan of using the Muonic Inducer to create a wave of devastastion to destroy the core of a planet.
- Galactus (David Kaye) - threatens the Earth for the Muonic Inducer the heroes stole from him
- Queen Veranke/Black Widow (Nika Futterman) - framed Weasel to take the fall for stealing Fury's brain scans to Tinkerer so he could have the Fold take control of Fury's brain to make him give access to all the S.H.I.E.L.D. operations, Hawkeye believes the time when she was asked as Fury's 2nd-in-command was the time when she infiltrate Russia to switch identities with Yelena Belova, the mission was to give the Skrulls access to all operations, revealed to be Veranke! She is the secondary antagonist of the game, assisting Thanos
- Maxwell Dillion (Skrull)/Electro (Jamie Foxx) - exposed in a flashback and killed, his corpse is only seen in the morgue with the Real Electro over his body raving about Skrull's he hates more.
- Ben Grimm (Skrull)/Thing (David Boat) - battled the Thing as boss one trying to frame him.
- Victor Creed (Skrull)/Sabretooth (Peter Lurie) - boss in the Vault trying to break out the Super Skrull.
- Angelica Jones (Skrull)/Firestar (Kimberly Brooks) - ???
- Carol Danvers (Skrull)/Ms. Marvel (April Stewart) - first boss in Manhattan in the Empire State Building.
- Odin (Skrull) (Frank Welker) - boss two in Asgard revealing he killed the real one.
- Otto Octavius (Skrull)/Doctor Octopus (Peter MacNichol) - boss revealed after the Electro Skrull's death, coming to capture the disobedient one, who was seen dead.
- Dr. Doom (Mark Hamill) - a herald of Galactus and a warlord whom was stripped of his immunity!