Peter and Mary Jane have returned to New York after a stay in Portland, OR (in Spider-Man: Final Adventure) at the request of Daily Bugle publisher J. Jonah Jameson to investigate the mysterious spider-man skeleton found in last month's Return of Kaine story arc. Ben Reilly, still believing himself to be the real Spider-man, has stolen the skeleton from the city morgue in order to discover who (or what) it really is.
Meanwhile, Ben's friend Seward Trainer has recently come out of the coma he has been in since the Cyber-War story arc back when Ben was still the Scarlet Spider. Seward, of course, is the geneticist who assisted with tests that proved Ben to be the original and Peter to be the clone (See: The Trial Of Peter Parker).
The story begins with Ben, as Spider-man, making a quick exit from Ravencroft (asylum for the criminally insane) where he has gone to investigate the recent sightings of a Carnage-like creature on the streets of New York. While learning that Cletus Kasady (the Carnage symbiote's host) has not escaped, Ben is forced leave fast when the police arrive (still wanting him for questioning about the stolen spider-skeleton). Peter Parker arrives in a nice new rental car, Ben hops in and the two make a hasty retreat from the police.
Most of the issue is told in the form of a conversation between Peter and Ben. We learn that Ben's girlfriend, Jessica, a would-be photographer for the Daily Bugle, is obsessed with Spider-man ... because she believes he murdered her father. However, just as Ben is about to learn more, he is interupted by a phone call from Peter, who suggests that they take the spider-skeleton to the Avengers to find out just who (or what) it really is. In a scene featuring Peter and Mary Jane, Peter reveals that he doesn't trust the results of Seward Trainer, Ben's friend, and wants to get the results from an un-biased source.
The conversation ends as Peter and Ben arrive at the Avengers' temporary headquarters just out of the city. While tests are being conducted on the skeleton, Peter uses a photo-enhancer to brighten a picture of Jessica and her father taken years ago. On the franc tic final page, we learn that the man who Jessica blames Spider-man for killing is actually the burglar who shot Peter/Ben's Uncle Ben ... and that the skeleton found at the bottom of the smokestack is a clone (which makes Ben and Peter ask: if that's the clone, what does that make me?)