Starting during the final days during World War II, a elite group of soldiers lead by Steve Rogers, a.k.a Captain America attacked a Nazi strong hold controlled by the human/atari hybrid, Herr Kleiser, who has built a destructive missle he intends to launch at Wasington DC. During a hard battle wtih Kleiser and his men, Cap is unable to keep the missle from launching but instead hitches a ride on it and lest Kleiser's castle self destruct around him. Captain America is able to disarm the missle over the artic but falls into the sea as the missle breaks up. During is final thoughts, he thinks of his girlfriend before disappearing in the deep.
60 years later, Cap's body is found frozen in ice by Betty Ross and Bruce Banner who have been assigned by SHIELD to recover Captain America's body and create a new super soldier program in the planet's effort to defeat the Atari race. A few days later after recovering Cap's body, Nick Fury, the head of SHIELD is having the final pieces of a defense satilite that will help fight against the Atari but it's destroyed just after going online by the alien race. Angry over the situation and not wanting to wait on the super soldier program, the World Council tells Fury to activate Project Avengers. A group composed to Earth's Mightiest Super heroes, something Fury isn't the most keen on. He starts by seeking out Janet Van Dyne and Dr. Hank Pym. While Jan doesn't have a problem, Hank has had it with SHIELD constantly screwing him over but Fury needs him non the less. Hank decides to accept Fury's offer and then shows his new ability to grow to giant size to show that he does a lot more than talk to ants as a super hero these days.
Meanwhile, Fury sends the Black Widow after Tony Stark to help convince him to have Iron Man join the group but Stark isn't too thrilled with having Iron Man join the team, saying he works alone. However, he's more than happy to help SHIELD out with some new weapon designs to help in his little war with the Atari. Not long afterwards, Bruce Banner and his group of scientists are working on Captain America's body which has now been defrosted. However, soon a pulse is found and Captain America springs to life but is disorented as a result of his 60 years and attacks all the SHIELD agents that try to subdue him. Cap eventually breaks outside and sees that he's in New York but not his time, he turns to see Fury and asks: "Did we win?" Fury answers: "We did son, we did." The next couple of days, Cap is filled in about what happened since he's been gone and that Fury wants him to lead the Avengers. While Cap is a bit hesitant, he soon agrees and learns about each member of his new team and about the truth of Bruce Banner who is secretly the Hulk.
Steve Rogers is filled in about what the world around him and he and Fury even go out to recruit, the Norse god of Thunder, Thor who is helping with some political rallies. During a drink at a bar, Thor openly rejects Fury's officer but seems to know Captain America better than he should after all these years. Not long after that, Steve decides to seek out his old girlfriend, who has now married James Barnes, his old partner, Bucky from the war. James tells Steve that it was hard for her all these years he was gone but Steve let's James know that he is happy that she married him. He then departs with her looking out the window.
A couple days later after starting to train with the Avengers, the Atari attack New York and the Avengers spring into action, including Iron Man who tries to help them out. During the battle, Iron Man's armor is damaged and he is revealed to be Tony Stark, much to Nick Fury's displeasure. The Avengers get the upper hand on the Atari but they soon attack a few days later and Fury, needing his new super soldiers orders Bruce Banner to move the program along but it's revealed that Banner never intended to use the super soldier program from the government but in an effort to cure himself but the experiment goes wrong and Banner turns into the Hulk again just as the Atari attack their base. Both Iron Man and Thor join the Avengers in fighting the Atari but even their numbers are still not enough against the alien warlords. Soon, the Hulk ends up fighting the Avengers during the battle until Betty turns towards the Atari and in doing so, starts destroying their ships with ease, leaving the Avengers to push back and defeat the Atari who quickly return to space defeated.
The next day, Fury congradulates the Avengers on a job well done but promises them that the Atari are hurt but more of their pride than their numbers. They'll be back and they will stop them. Not long after, Steve finally sees his old girlfriend, who he greets with a hug, saying she has missed him but knows that he always was meant for something more and Steve knods his head. Now with the world in danger, it's going to take Earth's Mightest to stop threats both wordly and outworldly, hence, the Avengers Assemble.