Wowwww!! This is really good!This is my idea for bringing Scott back he goes to Jean and explains his resurrection by telling her about Battle World and how he was bonded with the Phoenix there. He tells her when reality was restored it wasn't him but a near identical version of him from the Kingdom of Manhattan on Battleworld who came back and died. The Phoenix did bring him back but then left him probably searching for her. Once he got back he realized the world thought him dead and he also thanks to the Phoenix remembered the truth and that until the Phoenix freed him he had a piece of Apocalypse hidden in him it's been there since they merged he was never fully freed. A piece of Apocalypse was always there in the back of head nudging him where he wanted him Apocalypse wanted to divide the X-MEN. But that wasn't all, he's been behind it all all the strife in the hero community over the last few years when they forced Apocalypse out of Scott most of his persona left leaving only that small part to guide Cyclops. The rest went into clone bodies of his former form yes bodies he divided his mind putting the main psyche into a new body he created from Jean and Scott's DNA he stole while Cyclops. In the hybrid body he's been using it's telepathy to do to others what he was doing to Scott nudging them to his goals he was behind Scarlet Witch attack on the Avengers and the decimation of the Mutant Race. He was also behind the rift between the Avengers and X-Men and even behind Blackbolt releasing the Terrigen knowing it's effects on Mutants. He wants everyone fighting each other he's been behind the "Civil Wars" in the Hero community doing it all to create his world of survival of the fittest and now with Jean back it's up to Cyclops, Jean, and the X-Men to stop him.
Yeah very over reaching but I'd really love to explain why the heroes have been jerks to each other in the 21st century and perhaps make Apocalypse a real threat again.