The conspiracy is revealed in South Park: The Fractured But Whole as The Coon informs his fellow super heroes it all hinges on a missing local cat.
Cartman as The Coon is leader of Coon & Friends, which has already been teased as suffering from a civil war over disagreements on their billion dollar super hero movie franchise. The big conspiracy starts with a missing local cat and soon spirals out-of-control South Park style.
It seems 'future' Coon travels back to inform the boys 'living in the past' (from The Stick of Truth) that a terrible future lies ahead and that the only hope to survive it was to "assemble the team" of super heroes. I'm sure it had nothing to do with the $100 reward money for finding Scrambles.
As the returning New Kid we are once again nothing but a lowly Douchebag as we've never played super heroes with the boys before, and naturally all our achievements in The Stick of Truth account for nothing. Fortunately Cartman as The Coon reluctantly agrees to give us our 'tragic back story' as we join their ranks.
South Park: The Fractured But Whole releases on PC, Xbox One and PlayStation 4 in Q1 2017.