Marc Webb was going somewhere with his Amazing Spider-Man movies, but where exactly was never certain. He had a whole storyline running with Peter Parker's dad and weird bio-experiments and all sorts of other stuff that got cut short when Amazing Spider-Man 2 sucked and Sony cut a deal with Marvel to bring the character to the Marvel Cinematic Universe. Will we ever know the plan? I'm sure Webb will speak at some point, but in the meantime Denis Leary said some weird-ass shit that makes me think they were headed to the infamous Clone Saga.
Talking to IGN at Comic-Con Leary said he would have been back for the third movie:
"Possibly in 3, there was this idea at one point that Spider-Man would be able to take this formula and regenerate the people in his life that had died. So, there was this discussion that Captain Stacy would come back even bigger in episode 3."
That sounds nuts, but that also sounds a lot like the cloning in the Spider-Man comics. In the original stories Professor Miles Warren created a process that he called cloning but that actually turned already living people into perfect replicas of others; he would inject someone with Gwen Stacy's DNA, for instance, and that person would become exactly Gwen Stacy. He did it with both Gwen and Peter, and Peter battled - and killed! - his own clone. Years later it turned out that not only had the clone not died, but that the clone who had seemed to die might have been the real Peter Parker. He returned to Spider-Man's life, setting off a lengthy and terrible storyline that threatened to retcon decades of Spider-Man stories, all intended as a way to get Spidey out of his marriage.
The Clone Saga is perhaps the most infamous story in the history of the character; it dragged on for almost two years and it made a lot of longtime readers (like me!) lose faith in the comic. It was bizarre in a very bad way, and it has been largely brushed under the rug. But could this be the focus of the third film? Leary's statements make me think of Warren's cloning procedure, and it feels very much like this totally misguided movie series to tackle this storyline. It could have been a monumental trainwreck.
Maybe at some point we'll know the truth, but for now I think we just barely avoided a Clone Saga bullet.