Having escaped The Matrix, Peter was sent back in time to prevent The Matrix from happening in the first place. He succeeded, kind of, but then the future became CPAF, Section 9 became a thing, and all these people's cyberbrains started getting hacked. After having a beer with Hideo Kuze and Motoko Kusanagi he realized it was time to go back to the past once again to help secure VR so that the cyberbrains of the future wouldn't be used to hurt others through what became a common presentation layer attack vector.