Captain America, the Howling Commandos, and the Strategic Scientific Reserve managed to destroy many HYDRA bases across Europe and thwarted many of their attacks. Unable to locate Johann Schmidt and his headquarters, Captain America and the Commandos went to attack the Schnellzug EB912, a train transporting Arnim Zola.
In the attack, Gabe Jones succeeded in capturing Zola, but Bucky Barnes, Steve Rogers' best friend, fell off the train and down the mountain and was presumed dead. Zola eventually confessed to Colonel Chester Phillips that Red Skull was planning to attack almost everywhere on Earth, and gave out his location.
Rogers prepared to attack HYDRA at their headquarters with support of the Howling Commandos and the Strategic Scientific Reserve to infiltrate the base allowing being captured to masquerade a full frontal assault.
Red Skull managed to escape in the Valkyrie, and Colonel Phillips and Peggy Carter took Red Skull's car and used it to chase the plane and get Rogers onto it. Before jumping to the plane, Rogers and Carter shared their first and last kiss.
Rogers disabled most of the bombs and defeated their pilots, but as he was trying to stop the one for New York, he was stopped by a HYDRA Soldier and fell out of the Valkyrie with the bomb. Rogers managed to knock one of the soldiers into the propeller and eject the pilot. Avoiding fire from the plane's cannons, Rogers flew the bomb back onto the ship.
Grabbing his shield, Rogers headed for the bridge, where he was attacked from behind by Red Skull with a HYDRA Assault Rifle. Rogers blocked the blast with his shield and knocked the rifle from Red Skull's hands, dropping his shield in the process.
The two of them fought hand to hand and knocked the controls, causing the plane to plummet until Red Skull reengaged the auto-pilot. The plane leveled off and Red Skull fired at Rogers with his HYDRA Pistol. Rogers grabbed his shield and threw it into Red Skull's chest, knocking him into the Tesseract's containment device. Red Skull picked up the Tesseract, but the object opened a portal and launched him into it. The Tesseract melted itself out of the Valkyrie and landed in the Atlantic Ocean.
Even though Captain America defeated the Red Skull, the Valkyrie was still on autopilot, flying towards New York City. Rogers managed to contact the HYDRA Headquarters with a radio connected to the Valkyrie. The radio was answered by Jim Morita, but he was interrupted by Peggy Carter. He told her that he had to land the plane in the ocean. They talked until he finally crashed the plane into the Arctic. Howard Stark went looking for him in a submarine but only found the Tesseract.
66 years after these events, Steve Rogers' frozen body was found and freed from the ice by S.H.I.E.L.D.. When Rogers awakened, they tried to trick him into thinking that he was still in the 1940s. This trick failed and Rogers ran outside, discovering that he was in modern day New York. He met Nick Fury, who told him that he helped save the world in the 1940s.
In chronological order:
- Captain America: The First Avenger
- Agent Carter
- The Avengers (flashback)