Gwen is dead, and Peter may well be to blame.
Peter trusted Curt Connors, a doctor whose past experiments resulted in the Lizard and Venom, with a sample of his blood, which Connors explained could start a revolution in medicine and save lives. Connors then went on to use Peter's father's work on the experiment, coupled with some of his own genetically-enhanced DNA.
The result? A serial-killing organism that took Gwen's life, and now seems to be after Peter himself.
The organism, who, for lack of a better name, I will call Carnage, starts to resemble Peter again. Peter orders Connors back to his lab so that the doctor can find out how to kill it, threatening to throw it in a room with Connors himself.
What unfolds is a battle in the middle of the night where Peter blames himself for this creature. HUMAN pieces of garbage he can handle, but murderous, mutated clones of himself? Peter thinks he's failed completely, but has little more time to ruminate when Carnage attacks and kills two more cops. Carnage takes on a very familiar form, closely resembling Peter's late father.
Connors returns to his lab to find Peter waiting for him. Peter explains that the creature was looking for Peter to stabilize its own DNA (which is why it attacked the others). The face we kept seeing wasn't Peter's... it was Peter's father's face. Peter stopped thinking and let instinct take over. In a clear-cut case of him-or-it (emphasis on it: Peter didn't see it as any more than a spore or a virus), Peter threw the creature down a smokestack. Peter again threatens to kill Connors, but naturally doesn't follow up. Later, Connors goes to a police station and turns himself in.
The next morning, MJ asks if Peter caught the guy. Peter also announces that he's done with Spider-Man.
Ben Reilly shows up at work, and the dean tells him that his and Connors' experiment are what killed the guard (wait... Smitty? I thought his name was Sam.). Since Connors is in custody, the lab is closed, and Ben is out of a job. Ben asks if he can get his things from the lab. While no one is looking, Ben takes a test tube marked "Parker: Sample #2" and takes it, with a slight grin on his face.