So, seeing how Peter Parker is currently "alive" in Mile Morales: Spider-Man. People have been giving theories left and right about his resurrection and well, while I guess people have already thought of this, might as well give mine.
Since Brian Bendis is very aware that making Peter Parker a 'clone' is predictable, as alluded to by Ganke in MM:SM #2 my guess is this.
Peter Parker's apparent resurrection was caused by SHIELD.
Similar to how Phil Coulson was resurrected in Agents of SHIELD, Peter Parker was being resurrected under supervision of Nick Fury, considering all the guilt he felt and, if I recall, considered him as a son, tried all the resources they had to bring him back to life.
Fast forward a few years later (BTW, How IS Jessica still 16 if it's been a few years?), the entire Galactus event caused the shutdown of SHIELD caused Norman Osborn, whose also alive and well, to escape. Which also explains why Peter is alive. It's a bit coincidental that the Goblin returns due to the shutdown of SHIELD the same day as Peter.
Also, in the comic, Peter says that he 'doesn't want to talk about' how he returned, once again, mirroring Phil Coulson's resurrection in AoS whose resurrection experiment was so horrible and painful that he begged SHIELD to let him die.
Peter's experience either might have not been as painful or was mind wipped like Phil but still troubles him.
That is my theory and if you have one yourself, tell me!