Ultron and Sigma, with the Infinity Stones of Reality and Space, caused an event called "The Convergence", a merging of the Marvel and Capcom universes, with a single unified motive: bringing their worlds to perfection by purging them of organic life.
In the time since the Convergence, Ultron-Sigma has established a home on Xgard, the fusion of Abel City and Asgard. They command an army made of Ultron Drones and Xgardians infected with the Sigma Virus, which the fused androids hope to spread across this brand-new world and thus achieve multiversal domination.
88 days since then, a coalition of heroes from both dimensions, banded together to save their homes from destruction, stand in the way of this plan. On one end stands the Avengers: Captain America, Iron Man, Thor, Captain Marvel, Hawkeye, Doctor Strange, and an ally from the Guardians of the Galaxy, Rocket Raccoon. On the other stands their new cross-dimensional allies: Chun-Li, Dante, Nathan Spencer, Strider Hiryu, Sir Arthur, Chris Redfield and Mega Man X.
The coalition runs a full-frontal assault against Ultron-Sigma's army, acting upon intel suggesting that a prisoner inside the palace can help the heroes. A small group led by Chris and Doctor Strange infiltrate the interior, only to discover the prisoner is Thanos. Despite the reservations of those who have fought him before, the coalition takes Thanos with them as they escape Xgard—just after Ultron-Sigma joins the fray directly.
The heroes regroup inside Avengers Tower in the merged New Metro City; Thanos is detained in a new cell as the heroes hope to gain information about the remaining four Infinity Stones. As Iron Man and Dante come to blows with Captain America and Chun-Li over trusting their captive, Thor comes under the control of the Sigma Virus. The group holds off the crazed God of Thunder until he is recalled to Xgard by his new master. With no other options left, the coalition calls upon Thanos's adoptive daughter Gamora to persuade him into revealing what he knows. Thanos co-operates by telling the heroes where to find the rest of the Infinite Six.
The Time Stone is located in Valkanda, the fusion of Val Habar and Wakanda. Valkanda's king, Black Panther, and his new ally, a Monster Hunter, capture an intruder: Ryu, who was part of an expedition investigating abnormalities created by the Convergence. The only other person to survive the trip into Valkanda was "a scientist" — specifically, Bruce Banner, who intervenes in the situation as his alter-ego, The Incredible Hulk. Captain America and Chun-Li soon arrive to quell the hostilities between the others and ask for the Time Stone; Black Panther refuses on the grounds that the Stone powers a time barrier protecting Valkanda from intruders.
The situation changes when a host of Ultron Drones that were tailing the Avengers' Quinjet manage to breach that barrier. The drones soon unleash the Sigma Virus into Valkanda, which infects and ultimately awakens the Elder Dragon, Dah'ren Mohran. Hulk and Ryu rally to defeat the gigantic monster and save Valkanda from Ultron-Sigma's drone army. After being convinced that the Time Stone alone will not save his kingdom and that Ultron Sigma must be stopped using the rest of the Stones so the dangers of Sigma Virus can be neutralized, Black Panther gives the Time Stone to the other heroes. He and the Hunter opt to stay in Valkanda to keep watch over the kingdom.
The Mind Stone is hidden in a facility owned by A.I.M.BRELLA, the fusion of the Umbrella Corporation and Advanced Idea Mechanics. As per his request, Chris is sent in by himself to investigate the company's New Metro City plant. Despite his wishes, he is joined by Spider-Man, summoned by Iron Man to aid in the mission. Frank West later interrupts their work, explaining that his own investigation of monster sightings and disappearances—which includes him following Spider-Man—led him to the facility as well.
After fighting off infected soldiers and other experiments, the trio happen upon a series of test chambers containing more infected victims. Frank identifies a new entry as the mayor of New Metro City, Mike Haggar... who awakens from his coma and attacks Chris and Frank in a frenzy. Spider-Man ultimately stops Haggar, who recognizes the web-slinger as a friend; Haggar then explains that he was previously at City Hall before supposedly being kidnapped.
Further investigation leads the group to A.I.MBRELLA's leader, M.O.D.O.K. - who holds the Mind Stone - conversing with Jedah. Upon discovering the heroes, the android sends his B.O.W. army, including the feared Nemesis T-Type, to defeat the group. The heroic trio dispatches the bioweapons with ease and retrieve the Mind Stone—but they fail to seal away Jedah's portal, and the Dark Messiah soon unveils his secret weapon...
A trio consisting of Doctor Strange, Dante, and Arthur head into the Dark Kingdom, the fusion of the Makai realm and the Dark Dimension, to find the Soul Stone. Their entrance interrupts a battle between Ghost Rider and Morrigan Aensland, instigated by the latter's desire and attraction towards the former. As a former native of Makai, Morrigan points the heroes towards Jedah's old home, claiming that they can find the stone there. The group arrives to see Jedah feeding the souls harvested since The Convergence into a Klyntar symbiote, in hopes of stopping Ultron Sigma. As Morrigan attempts to reason with her fellow Darkstalker, Doctor Strange and Arthur take care of a distraction in the form of two old enemies: the dread Dormammu and the feared Red Arremer, Firebrand.
Despite Dormammu and Firebrand's defeat, the distraction proves successful, as the heroes fail to prevent the completion of Jedah's symbiote beast. Jedah, the beast, and the Soul Stone escape their grasp through the portal to the A.I.M.BRELLA faclity—where Spider-Man, Chris, Haggar, and Frank begin running away from the symbiote.
Back at Avengers Tower, Hawkeye, Spencer, Iron Man, and Dr. Light hold down the fort in relative peace. That ends when Ultron-Sigma leads a fleet of drones towards the tower. Hawkeye holds off a few of the drones on his own, but the armada breaches Dr. Light's shields, which gives Ultron-Sigma a way into the tower. Iron Man and Spencer hold off Ultron-Sigma as best they can before a desperation attack fueled by the Tower's power causes a blackout and accidentally releases Thanos from his cell. The two would-be gods battle; after Thanos cracks the Reality Stone embedded in Ultron-Sigma's forehead, the fused android feels pain for the first time and flees for repair.
One last away team—Rocket, X, Captain Marvel, Nova, Gamora, and Strider Hiryu—heads to Knowmoon for the Power Stone, which is in the hands of Grandmaster Meio, an immortal being whose plans for world domination have been repeatedly foiled by Strider Hiryu over the course of a millennium. Knowmoon was once the planet Knowhere; after The Convergence, Meio - who willingly works with Ultron Sigma - remodeled the planet into his old moon base. Captain Marvel lays out a plan of attack: volunteers Hiryu and Gamora will challenge Meio directly as a distraction while the remaining members of the group focus on sabotaging his Gravitron and reclaiming the Stone.
As Hiryu explains his previous experience with Meio to Gamora, Rocket and X come face-to-face with X's old partner, Zero, who has fallen under the influence of the Grandmaster. X soon returns Zero to normal. Captain Marvel and Nova appears late as they're found by Meio, who unleashes Ultron Drones on them while assisting from the background. After the drones are defeated, Hiryu and Gamora find Meio and swiftly assassinate him.
The heroes then remove the Power Stone from the Gravitron Core, but it is revealed to be a giant container for the Sigma Virus, which begins to plummet towards New Metro City.
As the Dark Kingdom away team returns to Avengers Tower, Chris and Spider-Man report their failure to stop Jedah's symbiote beast from getting loose on the streets of New Metro City. Spidey's familiarity with symbiotes gives him a one-up on the beast, so he tells his teammates to use fire and sound attacks to defeat it. Dante, Ghost Rider, Iron Man, Hulk, and Morrigan join the fray when Jedah begins looking for the Stones held by the heroic coalition. Right after, Captain Marvel's group report about the Gravitron and the Sigma Virus. Captain America also reports about the Time Stone, and Iron Man tells him to head back quickly to help.
During the melee against the Symbiote, an errant RPG shot from Chris nails the symbiote, which causes symbiote goo to fall onto and thus infect Spider-Man. Although Spidey temporarily turns on his allies, Frank's use of the environment soon dispels the black suit. Spider-Man heads toward Avengers Tower with the Mind Stone in hand as Ghost Rider and Morrigan fight Jedah to stop him from going after Spider-Man. After that, reinforcement arrives in form of Hulk and Dante, so Jedah decides to go to Avengers Tower to grab the stones there.
Meanwhile, Captain America's group arrived with the Time Stone. He and Hawkeye receive word from Captain Marvel and Nova about the Gravitron and the Sigma Virus coming closer, with Rogers telling the two to help the heroes on Earth and Stark also deciding to help other heroes fight off the Symbiote. Thanos offers Cap a solution... just before Jedah ambushes the group within Avengers Tower to claim the remaining Stones. The Dark Messiah fights off Cap and Ryu, but the latter falls to his inner darkness, the Satsui no Hadō. Before Jedah can strike Ryu down for good, Thanos intervenes—mostly out of curiosity in regards to the Satsui no Hadō—and overpowers the Darkstalker, forcing him to flee to his home realm.
After the rest of Knowmoon team arrives back on Earth and the Infinity Stones are gathered, the Gravitron Core is visible in the sky. Nova and Morrigan distract the symbiote while Doctor Strange redirects the Gravitron and Iron Man, X, and Zero harness the power of the Mind, Power, and Time Stones. As per Thanos' directions, the three heroes unleash a surge of that destroys the Gravitron and the symbiote—which also unleashes the Sigma Virus. The virus's spread was minimal, although the entirety of the coalition has been infected, which gives them only a short amount of time before they become soldiers for Ultron-Sigma.
3 months before, in her sanctuary, Lady Death is greeted by an interdimensional visitor: the Dark Messiah of Makai, Jedah Dohma. The universe in which Jedah resides has an imbalance of living beings compared to the deceased—as does Death's universe. Seeking an "equilibrium" through universal homicide, Jedah proposes an alliance with Death to cull souls from both universes. Death agrees, but says such a task will require six artifacts of great power—the Infinity Stones.
To pull off the plan, Death calls upon longtime suitor Thanos to aid their cause. She tells Thanos of her boredom with the universe and asks him to remake it using the power of the Stones, then bestows upon him the Space Stone. The Reality Stone rests somewhere in Abel City, a futuristic city within Jedah's universe that Thanos cannot enter. The Mad Titan recruits omnicidal android Ultron to help bypassing the Abel City's barrier and retrieve the Stone.
Ultron infiltrates the city and comes face-to-face with Sigma, the rebel Maverick who wishes to start an uprising for his species. Despite initial hostility, the two artificial beings discover a common bond—hatred of organic life—and plan a scheme of purging them off their universes. The two then fuse together: Sigma's progamming enters Ultron's body and creates Ultron-Sigma. The merged entity then backstabs Thanos, taking his Space Stone and using it and the Reality Stone to cause The Convergence.
They are all revealed inside Stark's dream, who fainted after the successful defense against the Gravitron, caused by the Time Stone.
The coalition regroups in Avengers Tower to put together a new plan. Dr. Light explains that they must still find a way to properly regulate the power of the Infinity Stones if they want to stop Ultron-Sigma, whose defeat should theoretically heal them from the Sigma Virus. Thanos proposes taking Iron Man and a small team to Sigma's laboratory in Abel City so they can create a device that will help them, while Dante offers to fight Jedah one-on-one for possession of the Soul Stone. The rest of the heroes will do what is necessary: a full-frontal assault on Ultron-Sigma directly in Xgard, all to hold him off long enough for Iron Man and Dante to pull off their parts of the plan.
While the coalition battles a Thor-led army of Ultron Drones and Xgardians, Dante arrives in the Dark Kingdom to challenge Jedah. Demon and demon hunter collide, and after activating Devil Trigger, the Son of Sparda emerges victorious. Dante takes the Soul Stone and spares Jedah; after the Stone reveals to Dante that the remaining Stones will not be enough to stop Ultron-Sigma, he leaves for Xgard, promising to do things "his way".
Meanwhile, Iron Man, Zero, Frank, Gamora, Ryu, and Thanos infiltrate Sigma's lab and retool Abel City's technology into a weapon. During their time alone, Iron Man reveals to Thanos that after using the Infinity Stones at Avengers Tower, the Time Stone showed him a "flashback": Jedah and Death's plan, Thanos's role in The Convergence, and the fusion of Ultron and Sigma. Thanos becomes enraged when he learns he was just a pawn for Death, then attacks Iron Man and Frank; although the duo succeed in temporarily subduing the Mad Titan, he recovers quickly, takes the two down and steals the Time Stone, who uses it to confirm Iron Man's claim.
Thanos soon beats down Ryu, Gamora, and Zero, then reveals his real reason for the trip to Abel City: the creation of a gauntlet based on Sigma's own handiwork, which Thanos uses to steal the Satsui no Hadō from Ryu. He tells the heroes that they can keep their special weapon—and their Infinity Stones—before disappearing. With Doctor Strange's help, the group rejoins the coalition in Xgard's throne room for the final battle.
The coalition manages to hold off Ultron-Sigma, his army, and the still-infected Thor. But the fused entity has a surprise for the heroes: He has possession of the Soul Stone. Dante steps foward and admits to betraying his allies by giving the Stone to Ultron-Sigma. But the android soon becomes overwhelmed by the power of the Soul Stone, which ultimately rejects them. Dante then reveals his plan: his battle with Jedah taught him that only those with powerful souls can handle the Stone—and since Ultron-Sigma has no soul to begin with, the Stone's power would be enough to stop them.
But out of the smoke and fire emerges a new monstrosity: Ultron-Omega. This new entity orders Thor to attack the heroes, but the Soul Stone frees the Asgardian prince from the Sigma Virus and restores his sanity, after which he rejoins the battle with his allies. Ultron-Omega captures and threatens to kill Dante, but Thor and X rescue the demon hunter as the Abel City infiltrators arrive for the final fight. Iron Man reveals the special weapon: the Infinity Buster, a large cannon powered by the four remaining Infinity Stones with which X can defeat Ultron-Omega. Dante, freshly free, aids Captain Marvel on beating down the fused being into submission both to protect X and set him up for firing the Buster. With the aid of his allies, whose strength is channeled into him via Doctor Strange and Morrigan, X loads the four stones into the Buster, dons his Ultimate Armor, and fires the weapon. The blast destroys Ultron-Omega for good.
...but the universes remain fused.
Doctor Strange hypothesizes that the damage done to the Reality Stone, which was one of the two Stones that created The Convergence, makes reversing that fusion an impossibility. For the foreseeable future, both worlds will remain merged. Thor proposes an Infinity Watch: Each of the Stones will be assigned to individual caretakers—two from Earth, two from Xgard, and two from the Dark Kingdom—to prevent another Convergence...or worse. The coalition agrees, then ventures forth into their new shared home, vowing to protect it together against those who would do it harm.
In a post-credits scene, Jedah talks with Death in her sanctuary, with the duo plotting a new culling—that is, until Thanos arrives armed with Sigma's gauntlet, the Satsui no Hadō, and a desire for vengeance...
