In the recent New Avengers series, several hundred super-powered criminals escape from The Raft (i.e. a prison for super powered criminals), although some are apprehended by Spider-Man and other super-heroes, including Captain America. In the aftermath of the prison breakout, Cap asks Spidey and the others to join him in reforming the Avengers. Resilient to become a member at first, Spidey finally accepts Cap’s proposition.

In Amazing Spider-Man #519, Peter, Mary Jane and Aunt May move into Stark Tower, headquarters of the New Avengers. While Aunt May and MJ gladly enjoy their new place of residence, Peter is rather uncomfortable with the idea of living there permanently. To make matters worse, in another part of the City, the criminal syndicate known as Hydra is planning to take over the world using some evil duplicates of the Avengers.

In Amazing Spider-Man #520, the New Avengers end up fighting these evil duplicates but are unable to stop them and the doppelgangers are able to flee. At issue's end, Spidey reveals to the others that he believes that the fights were meant to distract them, as part of a larger evil scheme to smuggle something into the country.

In Amazing Spider-Man #521, Peter comes to the realization – after rummaging around Tony Stark's computer database – that Hydra of old might be back. He conveys his worries to Captain America but the latter is rather unreceptive and demands to see some proof.

While attending an after-party for Mary Jane's off-Broadway play, Peter's spider-sense is set off by an individual spying on another one named Edgar Lascombe. Donning his Spider-Man costume, Peter follows the two men's vehicles across the City. A short time later, both cars stop in front of an apartment building in some residential neighbourhood. As the two men exit their respective vehicles, Peter/Spidey makes his move against the "spy". The spy, revealed to be a Hydra member, retaliates, guns blaring. But his outburst is cut short when he is hit by a car and killed instantly. Lascombe thanks Spidey, calls an ambulance and retires to his apartment, where it is revealed that he was too a Hydra member and that the dead man was his bodyguard.

While all this happens, MJ returns home (i.e. Stark Tower) and is accosted by tabloid photographer Vincent Chambliss. Fearing that Chambliss might figure out that Peter is Spider-Man, because of her presence at the Avengers Headquarters at that time of the night, she lies and tells Vincent that she is there to see Tony Stark.

Back at Lascombe's penthouse apartment, Lascombe dons his Hydra costume and makes his way into secret tunnels that lead to some kind of underground lair. He meets with terrorist leaders from various countries and explains that Hydra has planned to poison the Ogallala aquifer, the largest natural reservoir of water in the United States (providing water to eight States), using modified SCUD missiles carrying tons of the deadliest toxins known to mankind.

At issue's end, MJ's lies catch up to her when that morning's newspaper's headline mentions her secret rendezvous with Tony Stark at Stark’s Tower. This is where this issue picks up.

ACT 1: It is early morning at Stark's Tower, when Peter Parker's cell phone begins ringing. Slowly waking up, Peter takes the call. Daily Bugle editor, Joe Robbie Robertson, is on the other end of the line and tells Peter that he's sorry about what happened and that he's there for him. Slightly confused, Peter asks Robbie what the heck he's talking about. Robbie explains about the newspaper headline that says that Mary Jane is having an affair with Tony Stark. Hanging up the phone, Peter gets out of bed and goes out to find MJ. As he looks for her, he runs into Wolverine who teases him about the headline and makes a smart-ass comment about Mary Jane. In a matter of seconds, Wolverine is sent crashing through a window (with unbreakable glass) and falls to the ground several floors down below. Peter continues his search and finds MJ being comforted by Aunt May. Surprisingly, Peter is not mad with MJ and actually consoles her and tells her everything will be all right. Just then, Tony Stark walks in the room and offers words of encouragement to MJ; he tells her not to worry about Vincent Chambliss and promises to take care of him. Turning to Peter, Stark tells him about Lascombe's connections to Hydra and asks him to further investigate the latter. Peter puts MJ to bed – she hasn't slept all night – and takes off. Meanwhile, there seems to be some kind of romance developing between Aunt May and Jarvis, the Avengers' butler. Oh yeah, and Wolverine, shards of glass all over his body, returns from "downstairs".

ACT 2: Having donned his Spider-Man costume, Peter makes his way to Lascombe's penthouse apartment to spy on him. Hanging upside down from the balcony above Lascombe's, he observes the latter, who is sitting outside on his balcony. Just then, Lascombe's butler appears on the balcony and tells him that "it is time". As Lascombe makes his way back into his apartment, Peter/Spidey throws a spider-tracer that lands on his shoulder. Just then, Peter/Spidey suddenly starts feeling dizzy and briefly loses his grip. He falls a few feet but is able to grab onto a small parapet. Blaming it on stress, he shakes it off and tries to pinpoint where Lascombe went. Inside the apartment, Lascombe's butler leaves through the elevator, while Lascombe's disappears inside one of his rooms. Spidey waits and waits and suddenly realizes that his spider-tracer is telling him that Lascombe is going down, which doesn't make sense because the room that he's looking at is the only way out of the apartment to the elevator. Spidey decides to investigate this anomaly further and enters the apartment. He starts by searching the butler's room and finds a multitude of Hydra costumes hidden inside his closet. He then makes his way into Lascombe's bedroom, the spider-tracer telling him that Lascombe is nearby. Peeking around the room, he finds a small button on the wall and presses on it. This activates a sliding door, revealing a secret passage. While leaving a message for Tony Stark on his cell phone, Peter/Spidey puts one of the Hydra costume on and makes his way down the secret passage, which leads to this amazingly huge Hydra underground lair.

ACT 3: Making his way through this underground hideout, Peter/Spidey comes across Hydra members loading up trucks with weaponry, being briefed about what to do with their American stocks once the "plan" comes to fruition, and given rations that can last two weeks. Peter/Spidey continues walking around, trying to find out more about exactly what is going on. In an adjacent room, a higher rank Hydra member informs hundreds of members, standing in line, that this is their last chance to get their relatives out of the target zone. He tells them that, to evacuate them before reaching the critical stage of the plan, they will need their current addresses and phone numbers immediately. He reminds them that this is their last chance to get them out of these eight States before maxing out the quotas. Standing not far from there, Peter/Spidey wonders what could Hydra do to hit eight entire States. Just then, he notices the map displayed on a nearby large monitor and recognizes the Ogalalla Aquifer. As the wheels start turning in his head, a nearby conversation interrupts his thoughts. A young Hydra member is pissed off that his parents cannot be saved because maximum quota has been reached in Omaha, where his parents are residing. Taking off his mask, he tries to plead with the Hydra member in charge of registering names for the evacuation – who happens to be a friend of his – but his friend will not budge. Really pissed off, he pulls out a gun and points it at his friend's head, ordering him to get him out of there, to a place where he can call his folks. Unfazed by his friend's treachery, nor the gun pointed at his head, he tells him that there is not a chance in the world that this will happen. Just then, the Hydra members standing behind him pull their gun out and point them at him. Fortunately for him, that happens to be exactly when Peter/Spidey decides to reveal himself and make his move. He swings down, grabs hold of the young Hydra member and web-slings away with him. Immediately, the room erupts with gunfire and bullets zoom past Spidey and his hostage. The two land out of harm's way but the Hydra member punches Spidey. Spidey grabs him in a chokehold and tells him that, if he wants to see his folks alive, he'd better tell him how to get out of there and what's going on. Fearing for his life, the guy explains about Hydra's plan to launch a modified SCUD missile, loaded with bacilli, to poison the Ogalalla aquifer for the next hundred years, thus killing the entire Midwest region of the United States. Flabbergasted, Spidey asks the guy to point the way out. The man explains that the only way out is through the experimental genetics chamber and points towards it. Spidey grabs hold of the guy and swings in that direction. But, as he opens the door to the genetics chamber, his spider-sense immediately kicks in. Inside the chamber, the evil duplicates of Thor, Captain America, Hawkeye and Iron Man are waiting for him.

To be continued.