For the SECOND time in this series, it turns out that Peter Parker is "alive" within Doc Ock's memories. He was already "killed" once before, but comes back,
relives Doc Ock's entire life through his memories, then regains his own as Peter Parker. Instead of fighting Doc Ock for control of his body again, however, this time Doc Ock just suddenly up and decides that he's been defeated, straps himself to a machine, and erases himself from Peter's body, leaving Peter back in control.
This leaves Peter to clean up the mess,
which he does pretty easily considering that he's been "dead" and unaware of everything that's been going on for months of continuity. It turns out that the Green Goblin has changed his face and has been acting as a founder of Alchemax. Spider-Man gets a cure for the goblin virus and uses it on the Green Goblin, effectively erasing his insanity and super strength. He escapes and says he's going to change his face/identity again to keep fucking with Spider-Man, though.
And that's pretty much it. Maybe Amazing will cover the fallout in more depth, but with Superior, it's just Peter basically saying "sorry I was a dickhead" and people going "hmm...OK!"
Mary Jane and Carlie get the truth, but instead of sticking by Peter, they both give up on him and want nothing more to do with him. Makes no sense after they spent months trying to figure out what was going on and didn't give up.