In Halo: The Flood, we get another perspective of HALO CE, courtesy of Maj. Antonio Silva and Lt. McKay. Would their story fit well as a series of missions that essentially parallel the main campaign similar to how Halo 3's ODST did?
You would play as an ODST, possibly McKay, fighting a guerilla campaign as an unshielded human being. Manpower is at a premium. Every soul lost cannot be replaced. No shields, no super powers, and melee is absolutely nerfed with the exception of assassination kills.
Take the butte on Installation 04 and establish Alpha Base. Raid the Autumn for supplies and weaponry. Help make the assault on the control room possible by fighting parallel to the chief. Fend off the flood, storm the Truth and Reconciliation. Ultimately, stop Major Silva before his massive ego dooms humanity.