The game will immediately follow the events of Call of Duty: Modern Warfare 2, where Russia continues its invasion of the United States of America, and has also expanded its offensive to Europe, including England, France and Germany.

Dr. Doom and the Masters of Evil launc an attack on the S.H.I.E.L.D. Helicarrier U.N.N. Alpha. Nick Fury sends out a distress call to all available super heroes for assistance. Captain America, Thor, Spider-Man and Wolverine respond to the call. Along with the other heroes, they save the Helicarrier from the forces led by Scorpion, Bullseye, Winter Soldier, Radioactive Man, and Fin Fang Foom.

The game begins when an electromagnetic surge from an uninhabited island called Katorga-12, once held by the Soviet Union, damages an American spy satellite. A group of American soldiers, which includes the protagonist, Captain Nathaniel Renko, goes to investigate, when another surge disables their helicopter.

The story is set in the fictional town of Isenstadt, which the Nazis have taken complete control of in order to mine rare Nachtsonne crystals necessary to access the “Black Sun” dimension. As the game progresses, happenings in Isenstadt become stranger (German patrols are replaced by supernatural creatures, etc.)