A trailer released at E3 shows a military operation originating in Latveria, home of master villain Doctor Doom. "The story starts with Secret War. We're using Nick Fury's invasion of Latveria as a jumping off point. The rest of the story is derived from the consequences of those actions," states Dan Tanguay, creative director for Vicarious Visions.
The game will then follow the Civil War story arc: a fight between heroes and villains causes an explosion in Stamford, Connecticut. Killing 612 civilians (including a number of school children), the government labels this "Super Powered Negligence", and the public demand a Superhuman Registration Act. The government passes the act, and all meta-humans are forced to adhere to or disobey the law. In the game, players are able to choose between the Pro-Registration side headed by Iron Man and Mister Fantastic with Songbird following them, or the Anti-Registration side, headed by Captain America and Luke Cage with Iron Fist working with them. These heroes are locked into their specific side, but the other characters are playable on either side of the conflict. Multiple endings are available, and are determined by the side chosen at the beginning of the game. Tanguay stated that the story will follow into the aftermath of the Civil War.