This just seems too obvious. Here is my theory in tl;dr format:
Chief will be sucked into a black hole or some sort of time paradox thingabob to where he gets transported to the past during the Human-Covenant War. Cortana will still be stuck in the present, and just like Halo 3, she will sometimes show up on your screen to tell you about the present (future to MC) and all the destruction that is happening around her CORTANA MUST BE SAVED! So John goes back through all the Halo’s finding a way to stop all the devastating events from happening. John then gets transported back to the future via the time-travelling device Cortana worked on for hundreds of years future time and John is sent back to the present future to confront a rampant Cortana (she led you to your demise)
Honestly, this seems plausible.