Ultimate Spider-Man #39 (2003)

Peter has a heart-to-heart with Nick Fury in an attempt to retire as Spider-Man. That doesn't go as planned, so he tries to find out if Eddie survived. He's certainly gone, possibly through S.H.I.E.L.D. cleanup, and Dr. Connors has figured most of it out (though he's going to stay quiet about it, given the help Peter gave him back in "Ultimate Marvel Team-Up #10.")