Mary Jane has been taken to the Baxter Building in the hopes of curing her of Norman Osborn's Oz formula. Sue Storm takes Peter's "father" to the roof of the hospital and reveals to him that he really is a clone that has been altered and aged. Nick Fury continues to stall FBI Agent Henry Gyrich as Peter and the clones fight Doctor Octopus.
Doc Ock manages to kill all the clones with his newly seen powers over metal except for the female clone Jessica, Spider-Woman. Peter and Jessica manage to take down Doc Ock and the battle is over. Peter tells Jessica that he is going to keep his word and turn himself over to Fury. Not agreeing with this, Jessica leaves on her own.
As Peter goes outside, dragging an unconscious Octavius, an argument begins between Peter and Gyrich, the man responsible for Octavius creating the clones of Peter. The Human Torch arrives and informs Peter he needs to go with him to the Baxter Building.
Back on the hospital roof, the older clone of Peter, now accepting his fate and seemingly aging further, askes Sue to be Peter's friend. After she accepts, he dies.
At the Baxter Building, Mary Jane appears to have been cured. The combine intelligence of Reed Richards and Doctor Storm was enough to determine how to cure MJ. Peter declares his love for MJ after nearly losing her. Then Reed tells Peter that it is possible for them to cure him of his spider powers due to the similar nature of his powers with Osborn's Oz formula. The choice is his.