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At the start of this issue, the Molten Man breaks into the hospital where Ned Leeds was taken to at the end of the previous issue. While this happens, at a different part of the hospital a doctor is examining Peter Parker, who has just collapsed. The doctor is seconds away from finding Peter's costume when he hears the chaos the Molten Man is making, and runs off. Peter wakes up and changes to Spider-Man, noticing how weak he is, since the Molten Man's body is giving off radiation. The Molten Man rants on about how Ned Leeds discovered his secret, and fails to notice Spider-Man sneaking up behind him with a fire hose. Spider-Man blasts the Molten Man, who then manages to escape in the confusion.
Spider-Man goes to Ned Leeds's room, where he finds Ned babbling about glowing rocks. Spider-Man then heads to Mary Jane's apartment, where he overhears Liz Allan (who unexpectedly reappeared last issue) talking to Mary Jane about what she did after she graduated. Liz tells Mary Jane that she became a nurse to be closer to her stepbrother Mark Raxton, shortly after he became the Molten Man. However, Mark felt like a prisoner, and lashed out at Liz. After he escaped from the hospital, he found out (just as Liz and the hospital staff had) that his metallic skin was dissolving, and will do so until he dies.
Peter then heads to the Daily Bugle, where he is immediately yelled at by J. Jonah Jameson to go investigate a warehouse robbery. Peter heads to the warehouse, but no one will answer any questions he asks. Peter calls Ned, who tells him that the Molten Man is up to something involving radioactive isotopes. Peter works out that the Molten Man must have stolen some isotopes from the warehouse, in order to change himself back to normal. On a hunch, Peter changes to Spider-Man then heads to a museum, where he finds the Molten Man stealing some more radioactive rocks. However, he's still weak from their previous bout, and is put out of action long enough for the Molten Man to escape.
The Molten Man manages to get on a train, and disguises himself as normal by wearing an asbestos mask and gloves. However, his body has gotten so hot that it burns through the mask almost immediately, and he screams that it's all Spider-Man's fault. The Molten Man climbs off the train and attacks Spider-Man (who has caught up with him), telling him that if he had managed to steal that one more rock, then he could have reversed his mutation.
Molten Man then starts attacking Spider-Man in a fury, since his body is already starting to burn itself up. However, Spider-Man manages to grab Molten Man's bag containing his isotopes and rocks, and throws it off the bridge they're on into the water. Without thinking, Molten Man jumps off the bridge, but upon hitting the water, his body is too hot for it, and he is seemingly vaporized.