While a weakened Peter struggles in Ana's captivity, a team of heroes attempts to track them down and save the city. But before they can, Ana issues them a warning: evacuate or face their own destruction. What she doesn't tell them is that Spider-Man's transformation is now truly, horrifyingly complete.

ACT 1: New York City. Relaxing and having a beer on the rooftop of their apartment building, Randy Robertson and Big John Anderson are wondering what is going on when hundreds of helicopters come flying by, accompanied by several superheroes, flying alongside (Iron Man, Storm, the Vision). Down below, at street level, Detective Garrett and Captain Cleeland, along with New York’s finest, are in full alert mode. Inside the S.H.I.E.L.D. Headquarters, Colonel Nick Fury, Captain America, and members of various military agencies are gathered for the same common goal as the rest of them: finding the Queen's bomb before it detonates (in 5 hours).

ACT 2: Meanwhile, in the Queen's Hive, deep within Manhattan Island, the Queen is walking around accompanied by Spider-Man, whose transformation into a real spider is now complete (will now be referred to as "Spider"). She takes him to a control room where several people are hung upside down by some kind of weird web-like substance. She introduces him to Professor David Jaffe, the man responsible for her genetic alteration and for configuring the serum that brought about his mutation. It is revealed, through her conversation, that she abducted Professor Jaffe back in 1954 and that he's clung to life ever since. Seizing the opportunity, Professor Jaffe tells Spider that he is changing too quickly and that no one can withstand that kind of mutation. He also tells him that there is one catch to his genetic alteration: he's pregnant. Huh??

ACT 3: Unable to question Professor Jaffe – spiders do not speak after all and he's been turned into one – Spider follows Ana out of the control room and back into another area of the Hive. Suddenly however, Spider begins to ooze green goop uncontrollably. Ana is worried; she does not know what is going on. In a matter of seconds, it's all over – Spider collapses to the ground and stops breathing. One of the Queen's drones approaches Spider and confirms that he is dead. The Queen is devastated. Furious, she screams at the top of her lungs. She then turns over to a couple of drones standing nearby and tells them to prime the device so that it detonates ten minutes from then.

ACT 4: Things do not bode well for Fury and Cap when they get a message from Cyclops, telling them that he, Nightcrawler, and some soldiers are surrounded by hundreds of mindless drones, down in the subway system. Back at the Hive, the Queen is making last minute preparations in anticipation of the detonation of the bomb. Unknown to her is that Spider has begun moving again. Suddenly, a hand emerges from within Spider and a body (in the buff) follows; that of Peter Parker, covered in green goop. Kneeling down, Peter is in pain; even more so when his brain is suddenly filled with a million voices. As he grabs his head with both hands and pulls them back away again, a sticky substance dangles from his head to his wrists: organic webbing.

ACT 5: Yes. Organic webbing. It appears that Peter’s transformation into a real spider has left him with some new powers à la "Ultimate Spider-Man". Peter is freaked out at this new development. However, the scientist in him tells him that there has to be some kind of explanation. Keeping his cool, he notices his Spider-Man costume in a nearby locker. Walking slowly, he makes his way to the locker, unbeknownst to Ana, who is directing her drones to prepare the bomb. Suddenly, a nearby wall blows up, scattering the drones. The army starts moving in, accompanied by Cyclops and Nightcrawler. The Queen screams at her drones to detonate the bomb immediately, but Spider-Man intervenes and prevents them from doing so. Spidey tries to get to the bomb to stop the clock but Ana begins screaming, which momentarily incapacitates him. Spidey's will, however, allows him to inch himself closer and closer to the bomb. Suddenly, following a stream of new instincts, he starts reaching out to every insect for a mile around him. Spectacularly, he manages to get inside the mind of the Hives and he is able to extract the information necessary to disarm the bomb. As he does so – unexplicably – Ana somehow blows up and it appears that she dies.

ACT 6: Minutes later, at street level, both Nick Fury and Captain America have felt the sudden surge of psionic activity, the explosion that followed and the subsequent return-to-normal of the Queen's drones. Spider-Man suddenly shows up and tells them that the bomb has been defused and that the Queen is dead. After receiving some well-deserved thank-yous from Cap and Nick Fury, Spidey web-slings away and finds his wife, Mary Jane, on a nearby rooftop. He swings down to her and he tells her that everything is all right. When she asks him what happened to him, he simply replies that he's just made a couple changes. As he says that, he puts his hands up and shows her his new organic web-shooters.