Main Over-arching Story (based of the Vicarious Visions (PS3/PS4/Xbox 360/Xbox One/PC versions) Edit
The story begins one year prior to the Civil War story arc. Nick Fury, having called in some favors among the superhero community, leads a team of Iron Man, Captain America, Wolverine, and Spider-Man, among other heroes, on an unsanctioned attack on Latveria. Shortly after landing, the team finds an audio log Black Widow recorded about a powerful but unstable power source somewhere in the area. They track it to an old church and discover Electro manning a power station built inside the church. Electro attacks them, but is quickly defeated. The team leaves through the back door as Fury tries to contact his secondary Bravo team. While he struggles with that, the other heroes discuss the attack. Spider-Man expresses doubts about invading a foreign country, but Fury points out that the local authorities won't show the same level of hesitation. This leads to him flashing back to a meeting he never told the heroes about. In it, he told the president and his associates that prior investigations into several villains receiving tech upgrades from Tinkerer revealed that he's getting support from Lucia von Bardas, elected Prime Minister of Latveria. Fury stops his flashback as he and the team proceed towards Castle Doom, fighting any Latverian soldiers who try to stop them. As they reach the castle's main gate, Scorcher and Wizard appear and try to stop them. The villains are knocked out, and the team busts the gate open. By this point, Fury is still unable to get in contact with Bravo team, who he sends Wolverine and Spider-Man to rendezvous with while he, Iron Man, and Captain America advance towards the castle's main entrance. Wolverine and Spider-Man meet up with Bravo team and disable the main entrance's electric locks before moving on. Fury tells Bravo team over the now-restored local comm-link that long-range communications are still jammed, so they find and shut down the jamming array, thus allowing Black Widow to get in touch with them. Fury, Iron Man, and Captain America confront Lucia Von Bardas while Black Widow guides Bravo Team through the castle on their mission to shut down Tinkerer's lab. The team heads for the main core, along the way beating more soldiers, trashing more of Tinkerer's inventions, and overloading power conduits. After Bravo team disrupts the core and sets in motion a massive explosion, Tinkerer sends a tank-like robot to stall the heroes while he escapes the blast radius. The heroes demolish the robot and escape the explosion, as do Nick Fury and everybody else he brought on the mission. The castle and lab are destroyed, and Von Bardas is presumed dead as a result.
One year later, Ms. Marvel fails to check in after finding underground tunnels while investigating a suspicious gun-running operation. A team is sent in to investigate and gets ambushed by Latverian soldiers. After beating them, the team moves on and finds Ms. Marvel being interrogated by Shocker, who the team quickly beats. But he sneaks away while the team frees Ms. Marvel, who leads them to a lift that takes them to a factory being used to stockpile weapons. Once the team destroys the weapons, they continue to explore the factory and find Shocker, alongside Diamondback and Grim Reaper, who fights the heroes while the other villains go help whoever all of them are working for. The team beats Grim Reaper and goes after Shocker and Diamondback, trashing any Latverian tech they encounter along the way. Diamondback is spotted aboard a nearby cargo ship, and the team boards it to go after her. Then a cyborg Von Bardas appears just as the ship takes off with the heroes on board. The ship moves out as Von Bardas informs the heroes that she intends to destroy their home as revenge for what happened a year ago. Scorcher, Wizard, Shocker, and Diamondback operate large energy cannons that fire at New York. The heroes disable the cannons and knock out the villains, but Von Bardas activates bombs implanted in their armor and hers in an attempt to destroy New York once and for all. The heroes disable the bombs and knock Von Bardas out, but extensive damage was done to New York by that point. A news report is shown discussing the attack and revealing rumors about the attack being revenge for an unsanctioned attack on Latveria one year ago. According to the report, Fury went off the grid, command of S.H.I.E.L.D. went to agent Maria Hill, and the heroes believed to be involved in the unsanctioned mission refuse to comment to the press. Meanwhile, Captain America and Iron Man are cleaning up the attack's aftermath while discussing the mission. Iron Man admits that he suspected that the attack was unsanctioned before questioning who he'd trust between Fury and the government. Fury shows up and explains that that's why he didn't ask the heroes to make that choice. He then flashes back to the meeting where he told the president and his associates about discovering that Von Bardas was supporting Tinkerer. After he handed them the evidence, the president reminded Fury that Von Bardas went to great lengths to mend ties between America and Latveria after taking power with help from the American government, which sent her country about 72 million dollars worth of support in the past year. Fury expressed serious concerns about what that money was being used for, given the recent discovery. The president refused to hear Fury's countermeasures and claimed that he and his associates would handle the situation diplomatically. The flashback ends and Fury explains that he refused to tell the heroes the true reason for the attack as a way of ensuring that he'd take the blame should things go sour because of the mission. Iron Man responds with a repulsor blast, revealing that the real Fury is laying low somewhere else and used a robot to contact Iron Man and Captain America.
Shortly after that, they meet up with several other heroes and discuss the situation. Because of the attack on New York, Congress is considering a bill called the Superhuman Registration Act (S.R.A.), which would force everybody with powers to register with the government, whether they want to or not. According to Iron Man, it would essentially mean the U.S. government would get to tell the heroes who the enemy is, so they've got to stop it from getting passed. The plan is for Iron Man to speak about it at a Congressional hearing while Captain America rallies support from the people outside the Lincoln Memorial. But by the time they and the heroes accompanying them arrive in Washington D.C., it's already come under fire from a heavily-armed terrorist group. The heroes show up, defeat the attackers, and trash their weapon stockpiles. Deadpool shows up and attacks the heroes, loses to them, and offers to help them fend off the attackers. Maria Hill shows up and reveals that Titanium Man is thought to be leading the attack and has taken hostages. The heroes, aided by Deadpool, head into the subway station and defeat more assailants. They find Titanium Man, who sends more soldiers to attack the heroes while he leaves with a senator for a hostage. The heroes beat the attackers, save the hostages, including Stan Lee portraying New York Senator Lieber, and defeat Titanium Man outside the Lincoln Memorial.
Iron Man speaks to Congress and rides off in a limo, where Captain America talks to him about the situation. Iron Man expresses doubts about the S.R.A. being the least of the superhero community's worries if any other incidents happen, and Cap gets out of the limo. Three days later, the New Warriors are shown on live TV pursuing several villains. Among them is Nitro, who immediately activates his explosion powers and blows up a small town. A newscast from 12 hours after the explosion reveals that over 600 people died because of it. A newscast from a week later reveals that Congress rushed through passing the S.R.A. because of the explosion. Later, Captain America is shown aboard the S.H.I.E.L.D. Helicarrier arguing with Maria Hill about being ordered to arrest heroes just because they won't register. He refuses and escapes before S.H.I.E.L.D. agents can tranquilize him. Later, the president is shown in the White House bemoaning the fact that everybody resisting the S.R.A. now has Captain America for a leader. The president considers putting the S.R.A. off, but Iron Man offers to deal with Captain America. From here, the story branches off into two separate directions, and the side players choose determines what they do and who they fight for the next several missions:
- Iron Man leads Pro-Registration forces and S.H.I.E.L.D. agents in their efforts to find and arrest unregistered superheroes
- Captain America leads Anti-Registration forces, including former S.H.I.E.L.D. agents who defected to support Cap under the title "White Star", as they strive to get the S.R.A. repealed.
Several major events happen, regardless of player choice. Pro-Registration forces attack an Anti-Registration base. Mister Fantastic develops a high-security prison in the Negative Zone, accessible only through a small network of heavily-guarded portals, and uses nanite technology retrieved from Tinkerer's lab in Latveria to develop a means of controlling villains. That system is then tested by having nanite-controlled villains help Pro-Registration forces stop Anti-Registration forces from removing their allies from a prisoner convoy heading for Ryker's Island, home to one of the portals leading to the Negative Zone prison. The stories converge at a chemical plant owned by Stark Industries. Iron Man uses it to stage a fake disaster big enough to draw out Captain America and many of his allies. Once they get there, S.H.I.E.L.D. cuts off every potential escape route to ensure that they stick around. Iron Man approaches Captain America and tries to offer amnesty and convince him to listen to some peace terms. Captain America responds by using some small tech to short out Iron Man's armor, starting an all-out brawl between the two sides. In the midst of it, several nanite-controlled villains break off and attack the agents they were with before stealing bombs. One of the agents removes his helmet, revealing himself to be Nick Fury undercover. He approaches a small group of heroes and leads them to the out of control villains, who are rigging the bombs in an attempt to level the whole area and every hero in it. The heroes fight Venom and Green Goblin and dispose of multiple bombs after Fury disconnects them. But Venom stops Fury from disabling the last bomb, which goes off and injures several heroes, including the ones who helped him.
Since neither side of the war saw what happened, Fury ends up sending some of his robots to save them. While they recover, Fury tries to warn Iron Man and Captain America about the nanite-controlled villains blowing the place up, but neither side is willing to believe him. When the heroes come to, Fury explains the situation to them and convinces them to help him investigate what's going on. To accomplish this, Fury manages to enlist the help of Tinkerer, whose own nanite work was used in the creation of the nanite control system. But Tinkerer can't get a clear answer about who or what has seized control of the nanite hosts without access to the nanite control grid's networking logs, which are too well-encrypted to hack into from the outside without years of work. Since that would take too long, Fury suggests that the heroes get to a computer storing those logs and transmit them back to Tinkerer. Luckily, one such computer happens to be in Ryker's Island, which Captain America and his Anti-Registration forces are attacking in order to remove their allies from the Negative Zone prison. Fury's team shows up in the middle of the attack and goes for the computer while the guards are busy fighting off their attackers. But after being patched into S.H.I.E.L.D. comm frequencies, the team discovers that the S.H.I.E.L.D. agents are detaining any heroes not accompanied by Iron Man. Later, Captain America's forces pass through the Negative Zone portal before Fury's team can reach the computer, making them the guards' main targets. Fury's team encounters Maria Hill, who sends more S.H.I.E.L.D. agents to fight them and buy Iron Man the time he needs to secure the Negative Zone portal. The team eventually reaches the computer, but it's in the same room as the Negative Zone portal Penance is tasked with guarding. What's more, the entrance is locked up so tight that Hill's access card is the only way in. They track her down and get the access card. Hill sends more agents after the heroes, but they beat the agents and return to the portal room, where Penance challenges them. Fury's team beats him, saves him from some nanite-controlled prisoners he accidentally released, and sends Tinkerer the info he needs from the computer. This leads to the discovery that the nanite control network has become sentient and is likely to use its hosts to spread its influence to more targets and become more intelligent. Fortunately, only a few nanite-controlled villains are released at a time, limiting the network's spread. But if the whole group escaped lock-down, it could escape the Negative Zone prison and spread over the whole planet, adding all of life on Earth to its collective consciousness. Tinkerer reveals that making countermeasures against such a threat will require unused nanite samples, which are likely to be found in the Negative Zone prison. Unable to control one of his robots from such a distance, Fury warps in himself so he can help the heroes. Relieved to know that there are heroes who aren't too busy butting heads to protect the innocent, Penance boots up the portal for Fury's team to use and offers to help if they need it. Fury's team shows up and goes after a sample, with Fury heading for the prison's portal control room to make sure they can escape when they need to. The others reach a prime sample, but S.H.I.E.L.D.'s nanite control team skips startup protocols and uses the sample on Equinox in a rushed effort to stop the heroes. Fury's team beats him, finds another sample, and grabs it before it can be used. But right around that point, Captain America shuts down all power to the prisoner containment grid in an attempt to cover his team's escape efforts. This releases all the prisoners, including the nanite-controlled villains, who proceed to go on the attack and take out everybody in sight. Captain America and Iron Man bug each other about their mistakes, but Mr. Fantastic convinces them to put that on hold until they save everybody. Fury sends his team to meet up with them to help deal with the problem at hand. Once Iron Man and Captain America are caught up on the nanite situation, Fury's team heads into the prison to restore power to the portal, which got knocked out during the initial breakout. Along the way, they discover nanite hosts using their link to share powers, making this fight significantly tougher. The team beats several of them and moves on, only to find a nanite-controlled Grim Reaper trying to infect Luke Cage. Fury's team beats Grim Reaper, saves Luke Cage, who goes to help Iron Man and Captain America guard the exit portal, and grabs the nanite sample he would've otherwise been infected with. Fury tells them to hold onto the sample as a backup for their efforts to discover a nanite countermeasure. The team presses on and saves Firestar from more nanite hosts trying to infect her. Firestar is released and leaves to help Iron Man and Captain America while Fury's team takes a nearby lift to the lower levels and restores power to the exit portal. The team fights several nanite hosts on route to the portal, including Molten Man, Grim Reaper, Moonstone, Whirlwind, and Diamondback, but Nick Fury is forced to activate the prison's self-destruct protocols to keep the nanites from spreading to Earth. The Negative Zone end of the portal closes as Iron Man, Captain America, the team Fury brought in, and several other superheroes escape and appear on the other side, only to find Maria Hill and several S.H.I.E.L.D. agents aiming guns at them. Captain America points out that several of them need medical attention, but Hill is more concerned about making arrests and taking down the heroes. Iron Man declares that temporary amnesty is in effect for the sake of getting to the bottom of what just happened in the Negative Zone prison. He then points out that if Hill disagrees, she'll have a LOT of heroes to deal with. Hill reluctantly agrees and orders her troops to bring in medical attention. Three days later, a large funeral is held to honor the memory of Nick Fury and everybody else who was stuck in the Negative Zone when the portal closed and is presumed dead as a result.
The heroes Fury rescued from the chemical plant explosion then bring Iron Man, Captain America, and several others to the base where Fury brought them for recovery. Captain America points out that the lack of corpses or signs of an explosion makes it tough to tell what really happened after the portal closed. Mr. Fantastic reminds him that they won't be able to investigate without a working Negative Zone portal, which will take weeks to get up and running. But the fact that he's yet to detect any signs of the nanite collective's signal on Earth implies that Fury successfully kept the nanites away from Earth. Tinkerer has escaped by this point, so Mr. Fantastic is unable to work off of their combined nanite research. Suddenly, hundreds, possibly thousands, of nanite signals start popping up all over the planet. Further investigation reveals that the nanite hosts are infecting key targets all over the planet to limit the resistance faced. Iron Man comments on their methodical, well-coordinated movements and identifies the Negative Zone prison's portal system as a viable explanation for why the nanite hosts are moving so fast. In light of the situation, which is escalating to the point where everybody on Earth will be infected in a matter of days, the S.R.A. has been suspended to allow the heroes to work together to fight the threat. Teams are being deployed all over the worst, but reports indicate a massive nanite host incursion into the capital city of Wakanda, home to the world's only deposits of vibranium. A team is sent in to help Black Panther, ruler of Wakanda, defeat the invaders and restore his control of the country. The team arrives and establishes a comm-link with Black Panther, who reveals that the enemy has surrounded the city and is attacking it with siege cannons. The team meets up with a Wakandan guard and helps her take down the cannons, but a nanite-controlled Havok ambushes them on-route to the city. They manage to beat him, and the guard stays behind to keep tabs on him while the heroes move towards the city, which by this point has lost its defenses and is vulnerable to aerial assaults. The heroes move through the city, restore power to the defense-towers, and destroy all nanite host teleportation pods encountered along the way. The team then heads to the main palace, which is still unprotected. Along the way, they get ambushed by A-Bomb and Justice, who have been infected by the nanites. The team beats them and leaves them in the care of Wakandan guards before going to the palace grounds, the defenses of which are still offline. The team boots up the palace grounds defense-towers and takes a nearby lift up to the palace. Black Panther patches them through to She-Hulk in Stark Tower, which is being attacked by a large army of nanite hosts. The signal cuts out as the team arrives at the palace, and Black Panther tries to restore it. Instead, he ends up contacting Nick Fury, who survived and is now a member of the nanite collective, which calls itself "The Fold". Fury explains that the Fold seeks to end all conflict on Earth by adding everybody to its collective. The heroes in Wakanda turn down his offer, which would mean giving up individuality and thinking for themselves. Fury sends in a huge Fold invasion force to attack the palace. The heroes, alongside Black Panther, defeat the invaders and secure the palace. The Fold retreats and leaves behind Venom and Green Goblin, who are later cured of their nanite infection and agree to help get rid of the Fold. But the Fold gets more aggressive in spreading its network over the next few weeks. Several heroes are unaccounted for, making it likely that they were infected. In fact, several super-humans have been targeted for Fold recruitment. Fury's decades of experience in dealing with super-humans makes it significantly easier for the Fold to expand its power base now that he's one of them. Fortunately for the heroes, Fury lacks comprehensive knowledge about Wakanda, making Black Panther's palace a very effective temporary base of operations. But given how rapidly the Fold is spreading, it seems that the only way to stop them is to disrupt their heavily-defended network.
Iron Man, Mr. Fantastic, Yellowjacket, Goliath, and other brilliant minds begin looking into potential Fold network weaknesses. They discover that the Fold is setting up massive "repeater towers" at various points all over the world to help extend the Fold network's range. The towers form a grid that's adaptive and extremely tough to shut down entirely, so trashing them would be a waste of time and effort. But the nanite stasis signal created back when this was a simple villain control system might work if broadcast on the Fold's network. Since the network is too well-encrypted to get into from the outside, the best option seems to be taking over a repeater tower and using that to broadcast the signal. The only tower that can reach the whole network before the Fold could react is the one set up in Iceland, one of the first countries the collective took over completely. If the heroes can infiltrate that base and broadcast the stasis signal, it would paralyze all Fold hosts long enough for them to be rounded up and cured. A small strike team is sent in to enact this mission. They land as close to the tower as they can get without drawing attention and head for the base. Along the way, they beat more Fold hosts and trash some amplifier pods, which the Fold needs to send more troops to the intruders' location. Over the comm-link, Yellowjacket points out that the teleportaion tech is similar to what was used in the Negative Zone prison and Black Panther reveals that long-range sensors are detecting an incoming threat. The team reaches the entance and forces it open, only to be ambushed by Spider-Woman and Wonder-Man, who close the entrance and are in the Fold's control. The team beats them, reopens the entrance, and enters the base. But by that point, Fold-hosts have begun attacking Black Panther's palace. The team moves on and encounters a Fold-controlled She-Hulk. They beat her, but the teleporter pad they need to reach their target is offline. So the team uses and blocks other teleporters, fighting Colossus, Firestar, and other Fold-hosts along the way, before moving on. The team activates the necessary teleporter pad and uses it to move on. Soon, they encounter stronger Fold hosts and beat them before moving on. The team then encounters Tinkerer, who taunts them before teleporting away and leaving them to fight Whirlwind and several other Fold-hosts. The team beats them and uses a nearby teleporter to move on. The team reaches the base of the repeater tower and get ambushed by Tinkerer and several Fold-hosts, including some enhanced ones who protect Tinkerer from damage. The team beats back the army attacking them, forces Tinkerer to retreat via teleporter, and starts to upload the stasis signal. But Tinkerer stops the upload from the top of the tower. The team takes a lift up to the top of the tower, knocks Tinkerer out, and finishes uploading the stasis signal. The stasis signal works and, according to global reports mentioned by Black Panther, knocks out every Fold-host all over the planet. But before they can be cured, strange energy signals begin to channel through the network and converge at the top of the tower. Nick Fury then busts out of a nearby pod in nanite-based armor that lets him tap into the powers of everybody the Fold infected. Nick Fury fights the heroes atop the repeater tower using the powers of Electro, Havok, Firestar, Multiple Man, Bishop, and A-Bomb, but eventually he's defeated and knocked out. The scene then cuts to Iron Man and Captain America talking to a still-sore Nick Fury in his hidden base after he's cured and treated by Mr. Fantastic. Iron Man reveals that all the other Fold victims were cured and recovered fine, but Fury's recovery is going slower because he was infected with stronger nanites. Fury admits that he knows that and goes to apologize for his mistakes, but he's cut off by Captain America pointing out that there's plenty of blame to go around. Iron Man points out that there's also plenty of cleaning up to do. The three of them agree on this and on the fact that although things may never be quite the same again, they can change for the better.
The fate of the S.R.A. and the end-credits audio depend on who the player sided with:
- In the Pro-Registration ending, the S.R.A. is amended to let heroes voluntarily sign up for S.H.I.E.L.D. training without revealing their identities or mandatory police service, and Iron Man takes over as commander of S.H.I.E.L.D. before speaking to the public about superheroes being people who can accomplish great things by choosing to work together more out of trust than by fear or force. The end credits for that scenario include a radio broadcast where a speaker hoping to talk to Bruce Banner about the aftermath of the Fold's defeat ends up talking to Hulk, who then trashes the studio after getting mad about not getting a trophy or parade for helping the other heroes save the world.
- In the Anti-Registration ending, the S.R.A. is repealed, the president grants full amnesty to everybody who worked with the Anti-Registration movement, and Captain America gives a speech at a Lincoln Memorial rally. In it, he talks about the Civil War making heroes lose sight of their main responsibility, helping those in need, and that the Fold crisis serves as a reminder of the importance of both individuality and working together when necessary. The end credits for that scenario include a segment where Deadpool complains to one of the game's major designers about not being mentioned in the title and not being more powerful than the other playable characters. Deadpool goes for his swords, but by that point the game designer has already edited the game's code to disable them and all of Deadpool's other attacks and powers. Deadpool gets angry, but the game designer threatens to completely remove him from the game. Deadpool leaves while muttering to himself about the situation and his plans to regain his powers and show the game designer just how few hit-points he really has.