The Biker Twins, rob an armored car then throttle up their motorcycles for a clean getaway until Spider-Man intervenes. However Spider-Man is surprised at how smart they were in plotting the robbery. At the Empire State University campus Flash flaunts the fact to Mary Jane Watson that he doesn't have to study anymore because he has landed himself a tutor. What a surprise when Flash learns that his tutor is actually Dr. Zellner who is actively testing his new Brain Booster the first subjects being the twins with substantially impaired IQ. Flash's fame evolves from athleticism to intellectualism as he charms members of the female student body with his wit and knowledge of language and recitation of Shakespeare. However, soon it becomes obvious that there are physical side effects of this smart serum. The Doctor is stumped as to why this is occurring and decides that he find an antidote via a more intelligent candidate, Peter Parker. The twins continue to have Dr. Zellner pump them full of the Brain Booster in an effort to pull off more elaborate crimes that only Spider-Man stop along with rescuing Flash from the Doctor.

The Gaines Twins, Roxanne and Roland have brain-blasted Spider-Man into believing that Mary-Jane Watson has died at the hands of Kraven the Hunter. Convinced by Frank Elson, a mysterious stranger, that the only solace is revenge, Spider-Man now tracks down Kraven in order to pay him the identical fate he inflicted on MJ. Part Two begins with Kraven drawing his final breaths under Spider-Man's might. Moments from delivering Kraven the final blow, Spider-Man notices that the surroundings don't mesh with some of his more recent memories. Combine that with a few of Kraven's conflicting syllables and Spider-Man determines that his reality has somehow been tampered with. The questions is, how or more like by whom? The Gaines Twins are behind everything and while Spider-Man seeks them out to confront them. During the confrontation it looks like Spider-Man is winning as he frees MJ from their grasp. Things take a turn for the worse when the twins use their mental power to trick Spider-Man into harming Indy. After this, the chatter (along with the rest of New York's sentiment) is all anti-Spider-Man and unfortunately a grief stricken Peter Parker agrees. This leaves Spider-Man one last obligation. He tracks down The Gaines Twins at a propane factory where their end is nothing short of explosive. Lastly, a spiritless, dejected, and morose Peter Parker tightly packs up his Spider-Man suit and throws it into the Hudson River allowing it to sink into the murky depths. Is this the end of Spider-Man? Or a new beginning for Peter Parker?