Peter's professor, Doc Connors, injects himself with reptilian DNA, which slowly changes him into the angry, vengeful Lizard; and since the serum affects Doc Connors' brain, Spider-Man must stop his beloved professor as he begins seeking revenge on those who have harmed him, including Harry.

A team of three ex-KGB agents called Pterodax take people hostage, including Peter and Indy, his new crush. They want Spider-Man, so Peter must figure out a way to appease Pterodax without revealing his alter ego.

Dr. Zellner tests his "smart drug" on Peter Parker foe Flash Thompson, and Flash immediately displays dramatic spikes in intellect. However, along with the IQ boost comes a potentially fatal side effect. With only minutes to find an antidote, Zellner takes Flash's suggestion that he experiment on an already intelligent candidate: Peter Parker.

The Gaines Twins, a brother and sister with uncanny telepathy, escape from an armored transport convoy, but Spider-Man apprehends them by overcoming their brain blasts with his own superhuman will power. Later, just as Spider-Man reveals to MJ that he's really Peter Parker, Kraven the Hunter confronts Spider-Man. As payback for the years he spent in jail, Kraven attacks MJ with one of his poison darts. Spider-Man rushes to her side too late, as her life slowly slips away. Now, Peter is out for revenge.

Spider-Man realizes that the diabolical Gaines Twins have brain-blasted him into believing that MJ has died at the hands of Kraven the Hunter. He corners the Twins, but things take a turn for the worse when they once again use their telepathy to trick him.