I predict Cortana, considering that freak out, to place a good number of missions only on Requiems land and water. She's an AI, so it'd be best not to piss her off at the especially wrongest ever time.
For the actual story, the Chief has a bizarre physical ailment just randomly pop that causes him to hallucinate (such as back at Halo 3's beginning)
Earth has a resonant connection to Requiem and this presents a problem, of course. If we need so badly in destroying the Forerunners worst kept secret since Halo (and that Prisoner of Charum Hakkor incident) how does history play out? In backwards. Requiem's no more and Earth falls dead.
Master Chief suddenly flashes back to Epsilon Eridanis, trickling little secrets of his past.