It's in hardcover #3, the whole Venom thing. The plot at the back by Bill Jemas tries to turn your sympathy towards Eddie by making him an innocent in it all, and yeah it's Peter who screws Eddie over by using him to get into the university labs. Eddie and Gwen are in love in it, but Gwen's father dissaproves (which doesn't work at all since Captain Stacy was dead by this point). It's quite a rubbish plot, actually. It ties Venom's origin into Spidey's webbing as well, which sucks, because it makes Venom ever present in the comic thereafter.
There isn't another script for it, it's Bendis' first plot for it - with comments by Jemas and Joe Quesada. It's not much different from the story that was printed in USM #33 - 39, though.