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?)
Ben and Peter discuss what the results of the skeleton might mean as they return from the Avengers' headquarters. Both begin to question what the new discovery means about who/what they are.
Meanwhile, Carnage's symbiote has indeed escaped, though without his host (Cletus Kassidy). After several pages of fighting with Spider-man and anyone else who gets in his way, the symbiote leaves its current host body and bonds with Ben, forming a sort of "Spider-Carnage."
However, the Carnage situation seems to take a back seat in this issue (despite taking up most of the story) when Peter goes to see Seward Trainer in the hospital. Seward refuses to see him--because of a phone call he receives just as Peter is entering the hospital. The man on the other end of the phone call? A mysterious, shadowed figure in a car just outside the hospital. In just one short page, the clone saga has suddenly taken a whole new direction.
Ben in the midst of an inner battle with the Carnage symbiote, but quickly switches over to a touching scene in which Peter struggles with his own inner demons over the whole clone situation.
Shortly after, Peter goes to see Ben (who, by this time, has made it back to his apartment) and they get into an argument over Seward Trainer. Ben trusts him unquestioningly, and does not react well to Peter's comments that there might be more to the situation than they know. Under the influence of the Carnage symbiote, it takes all of Ben's will-power not to strike out a Peter.
Peter leaves Ben and heads over to the hospital to get some answers from Seward, but finds that Trainer had already checked out. However, he does learn that something called the Multivex Corporation paid all of Seward's medical bills.
Meanwhile, Ben, as Spider-Carnage, is wreaking havoc on the hospital roof, and there is a confrontation between a powerless Peter and an extra-powered Ben. Peter barely escapes with his life when Ben temporarily regains control, but when Ben's reaction to Seward remains the same, Peter vows to learn the truth ... no matter what.
In part four, the Seward Trainer mystery deepens (and confirms our suspicions that something sinister is going on here) when Peter goes to the Multivex Corporation to see if he can find Seward. He is denied any information, but the actions of those working for Multivex solidy his suspicions. Meanwhile, we catch a glimpse of Seward Trainer in a darkened room speaking with a shadowy figure, who tells Trainer "I'd prefer you had privacy to continue your work ..." And so it appears that the clone saga is far from over.
Elsewhere, Ben returns to Ravencroft to try to find some answers about the symbiote from its original host, Cletus Kassidy. After a rather long and draining inner battle, Ben frees himself of the symbiote (which a weakened Kassidy finally gets to return to him). Ben is upset that he couldn't control the symbiote within him, but is heartened by the encouraging words of John Jameson, security chief at Ravencroft, and the issue ends with Ben feeling a bit better about his role as Spider-man.