The Ultimates capture Electro and Kraven the Hunter. They detain them in a maximum-security S.H.I.E.L.D. superhuman prison beneath the Triskelion, along with Flint Marko (the Sandman), Otto Octavius (Doctor Octopus) and Norman Osborn (Green Goblin). Nick Fury informs the five captives that they are detained because they have illegally altered their genetic code. Osborn is convinced that "There will be six" prisoners.
Otto Octavius wants to cooperate with his captors and is granted access to a laboratory, where his metal tentacles are held. He wills his tentacles to attack and then shuts down the prison's power, releasing the others.
Nick Fury immediately sends agents to collect Peter Parker, in case Osborn goes after him. Fury introduces him to the Ultimates, who do not believe that Spider-Man is a teenager, and reminds them that he has defeated all five escapees on his own. From a secret retreat, Norman Osborn places a call to the Chief of Staff in regard to Nick Fury.
The President chews out Nick Fury in regard to the call from Osborn, who blackmails the government or he would publicize his treatment at the hands of S.H.I.E.L.D.. Fury dispatches the Ultimates, however, the five escapees then attack the Triskelion.
S.H.I.E.L.D. takes Spider-Man's Aunt May into protective custody while Fury and the Ultimates pick up the pieces at the Triskelion. The escaped villains have abducted Peter Parker who was in costume, and unmasked. They tie him to a chair, and Kraven attacks Peter but Otto subdues him. Osborn humiliates Peter by recounting the accident that created him, and that he and Otto were Peter's parents in a way. Osborn then tells Peter that they will attack the White House and he wants Peter to join them. Peter refuses, and breaks free. Osborn then threatens Aunt May and Mary Jane if Peter does not join them. The six attack the White House, but a S.H.I.E.L.D. helicarrier arrives on the scene.
The six and the Ultimates battle it out on the White House lawn. Captain America tells Parker that his aunt is safe, and he turns on the Green Goblin. Goblin attacks Captain America, when his son Harry appears on the lawn, asking him to stop.
While Harry talks to his father, the Ultimates bring him down. Harry tells Peter that he will kill all of them for what they did to his father. All villains are detained again and Peter Parker is reunited with his Aunt. Captain America and Nick Fury talk about how the next war will be a genetic war, and that the people in power decide what the wars will be fought over.