1: Peter gets captured and tortured by HYDRA.

2: Peter and the Ultimates are HYDRA super soldiers.

3: The Avengers get hurt and out of commission, Spider-Man (and maybe his team) fill in for them.

4: Peter is an agent of SHIELD

5: Spider-Man gets hurt and almost dies, staying in a coma for weeks in the Avengers' tower.

6: Spider-Man becomes a wanted criminal because of JJJ

7: Spider-Man gets attacked by HYDRA and gets poisoned, Tony Stark and the rest of the Avengers are helping him get better

8:Peter becomes homeless and later fully stays in suit until his fast metabolism starved him and he needs help

9: Spider-Man and his team, The Ultimates, go missing and NYC goes to Crap without them

10: All or parts of the above stated ideas mixed together