Lt. Figgnuts said:
Quickie version, someone else can explain it to you more in-depth I imagine:
Pete gets into an argument with Kitty, and later encounters the Scorpion at the mall. During the battle the mask is damaged, and the face underneath is none other than Peter Parker. Meanwhile, someone kidnaps Mary Jane from her room. (USM #97)
Peter takes the Scorpion-clone to the Baxter Building to the Fantastic Four to analyze. Peter Parker reveals his identity to the group and then runs home so as not to be late. When he returns he discovers MJ's disappearance. Panicked, he runs to "the spot" where he encounters a girl with spider-powers (Spider-Woman). They tussle briefly, and she leaves. For some reason Pete return to his old house in Queens, where he finds a very confused Gwen Stacy. Meanwhile, Mary Jane awakens, captive in the old OsCorp facility. (USM #98)
The Fantastic Four attempt to communicate with the Scorpion. He mentions the zoo, wondering if he's returned there and mentions that there are others at the zoo. Scorpion tries to escape, and Reed decides that this situation is too big not to bring in Nick Fury, despite protests from Peter in the previous issue. Mary Jane's captor - who turns out to be a deformed Peter Parker clone - tells MJ that he's going to give her super-powers so that he won't have to worry about protecting her anymore. A dumbfounded Peter tries to figure out what to make of Gwen when Aunt May arrives. Aunt May freaks out and Peter reveals that he's Spider-Man to her. Richard Parker enters and asks her to calm down, and May speaks to him as if she knew he was alive already. Meanwhile, after being informed of the clone situation, Nick Fury assembles a team to go and take down Peter. (USM #99)
It's revealed that Richard Parker never actually died because at the last second, Richard chose not to get on the plane that later crashed, killing Mary Parker and the Brocks. After that he was recruited by a government splinter cell hoping to monitor Nick Fury's actions and take him down if necessary. He is unable to resume his old life or inform any of his relatives that he's still alive. At one point he goes rogue and approaches May, who flips out on him and tells him to stay away from Peter. This is around the time when Nick Fury shows up, and things go nuts. Gwen transforms into Carnage and leaps out to battle the soldiers, and May's heart gives out. Meanwhile, at OsCorp, the Deformed Clone is confronted by a Six-Armed Clone. The two fight, and the Deformed Clone is victorious. He then resumes his experimentation on Mary Jane. (USM #100)
That ended up being more in-depth than I wanted it to be. But there you go.
Issue 100 was issue 100.
So I'm kinda glad I didn't spend any money on USM 100.
I believe in accuracy for new people who may be curious.
