Wow this was an emotional roller coaster. Great job.

:) Great story, again. I don't think it needs an epilogue, because the last chapter felt a little bit like one. The variety in the story really surprised me, it went from depressing to happy so quickly :) - Coal.

I feel a bit stupid, but why is Tony dying? Because first it was palladium, but that got cured... Could you maybe clear it up? 'Cause I have no clue :) - Coal.

ending sorta confused me. thought the serum gwen gave him changed him completely back to peter parker so he wouldn't be spider-man at all anymore. either way, good story.

I'll have to agree with Marz1. Mostly with the universes and the dialog. I'm a lil' confused on the former and latter is more advice. There is not much detail given when they are talking. Just the little things like sighing, snorting, panting, etc.

Like "I am so over this!" Peter sighed in exasperation.

It gives more life to the story. :3

I vaguely remember the episode of the cartoon you are referring to, though its been years and years. You should depend on people remembering it to establish your setting though. Spider man and Banner are just kind of hanging in the middle of nowhere. I think this could use revision, maybe with some background for spiderman and the avengers, so we know why they don't get along. Since you are combining the recent spiderman movie and the old cartoon you need some more set up so we know which reality we are in. Also i think you need a little more work on the dialogue, since you haven't really captured the individual voices of the characters.
Keep at it!