The chaotic nature of the Scarlet Witch's mutant powers eventually cause her to have a mental breakdown. This prompts her to remake the world into one in which mutants are the dominant species. The heroes eventually force her to face the truth and return the world to its previous state. Unable to find happiness in any reality, Wanda uses her powers to drastically reduce the mutant population and eliminates the mutant gene.
In this world, however, she goes one step further and de-powers all of Earth's super-humans.
Once reality is restored, the Avengers and X-Men are unsure of the events that have transpired. All those with super-human abilities are immediately reduced to a regular human. There are some that benefit from this new status quo. Cyclops, The Thing, and Black Bolt who were prisoners of their respective powers, face a new life without restrictions. However there are those that are not so fortunate. Captain America dies quickly once the super solider serum is removed from his bloodstream. The rest of the formerly powered individuals experience various levels of relief and regret. Peter Parker seems to be the most grateful as without power, he is without responsibility.
Two months later, a small band of technologically-powered villains (Vulture, MODOK, Shocker, Stilt Man) assault the Kronas Building in search of the Cosmic Cube. The unique structure of the Cube allowed it to survive the great de-powering. They find the Winter Soldier aka Bucky Barnes waiting for them with a message: "The Cube isn't here".
Barnes survived the drone plane explosion and was brainwashed by his Soviet captors. He is kept in cryogenic suspension until needed for specific missions. He is currently under the control of Aleksander Lukin, who is the unwitting host body for the Red Skull.
Lukin unsuccessfully tried to acquired the Cosmic Cube from the Skull through normal means. When these methods failed, he had Barnes kill him. As a last ditch effort, the Skull used the power of the Cube to transfer his consciousness into Lukin, forcing them to co-exist in one mind. When the Skull takes control, he wears a mask that resembles his distinctive face.
While they fight it out, Iron Man arrives and captures all of them. As the only active super-powered hero, he is working for S.H.I.E.L.D to apprehend any villains that remain. He feels that something will happen to fill the void created by the de-powering, even if nobody believes him.
Iron Man's theory proves to be correct as the Red Skull unites The Hand, Hydra, and A.I.M under his banner. Within six weeks, he is leading his army in an assault on the Baxter Building, killing Johnny Storm, Ben Grimm, and Reed Richards in the process. He takes the weaponry Richards confiscated from Castle Doom when the Fantastic Four (literally) trapped Doom in Hell and assumed control of Latveria. Later that night, he makes a televised announcement from the Baxter Building that New York will be destroyed. The deaths will fully charge the Cosmic Cube and allow him to remake the world as he sees fit, creating the Fourth Reich.
At this point Iron Man and his armored allies (James Rhodes, Ms. Marvel, Wolverine, Falcon, and three unidentified heroes) arrive and attack the Skull and his forces. The remaining X-Men (Cyclops, Colossus, Storm, Kitty Pride, and Gambit) make their way to the Baxter Building to assist. At the appropriate moment, Peter Parker arrives and steals the Cube from the Skull, smashing it against a lamppost. He reminds the crowd hiding from the battle that they can and should stand up for themselves; it's their responsibility to fight against maniacs like the Skull. He then shouts out the rallying cry of "Avengers Assemble" and leads the New Yorkers against the Skull and his army.
Thirty years later an elderly Tony Stark and Peter Parker meet at Avengers' Mansion to commemorate their victory against the Skull. Tony arrives alone, Peter with his daughter and granddaughter. Tony voices his concerns that there may be a threat that humanity can't handle. Peter reminds him that if the need is great enough, humanity will rise to the challenge. As he says this his granddaughter begins to exhibit spider-like behavior.
First of all, I have a complaint with the way in which they killed Captain America. The super-soldier serum in his bloodstream kept him at his peak and young. Aging him "decades in seconds" as they stated doesn't make any sense. Having the serum removed from his system would cause him to age, but it wouldn't kill him instantly. The serum affects his physiology, not time itself. It is clear why Cap needed to be out of the story, but they should have removed him in a different manner.
With the powered individuals out of the way, one of the natural choices for a villain in the story was the Red Skull. One would think that Dr. Doom would have been selected. However they chose a point where Doom was trapped in Hell, making him unavailable. This particular fact was not mentioned in the story. I find this to be disappointing as that would have addressed three issues: (a) why the Fantastic Four took over Latveria (b) why Doom didn't stop them and ( c) why Doom isn't the featured villain in the story.
Without Captain America to occupy him, the Red Skull was free to accomplish his life's ambition: take over the world and convert it into a Nazi state. His method of choice is the ever-popular Cosmic Cube, which can change reality to suit the whim of the owner. The result is usually one of two options: the Cube is either lost or destroyed only to be found or repaired later. Not that this is a bad thing.
3.5 webs. With a few exceptions (noted above) the story was very enjoyable. The plot was solid, it progressed very well, and had believable dialog. My only real complaint was that the characters looked elven in their close-ups. That may be Pantalena's style, but it became very annoying very quickly.
The scene in which Peter inspires the crowd to fight back against is of course the showpiece and it is quite effective. Plus it's just really cool to see him scream out "Avengers Assemble".