I'm guessing that the mystery Arc will be SHIELD vs. Peter...
That, or, if im right about the whole "Deadpool was the mercenary who took down the plane with Peter and Eddie's families in it" idea... Then peter will find that out in the two part arc. Possibly that it was SHIELD who took out his parents.... Then Peter goes nuts, tries to take down those resposible, and then Spiderman is suddenly wanted for arrest. Aunt May would find out, he wouldnt have a home, and the Ultimates would be scouring the streets for him....
Then we have the interesting situation of "what does Matt Murdock do when he catches Spider-Man before SHIELD". I'd bet he helps...
But this is all wishful thinking...