Master Chief would fight his way to the shield generator, getting most of the rebels killed in the process. He'd deactivate it by pressing a button, which would somehow also release the Flood. He'd then learn that the Death Star was actually an anti-Flood weapon that works by destroying all the planets in the galaxy, leaving none for the Flood to overwhelm.
After that he would fight his way through hordes of Flood and Stormtroopers to get to the Death Star's reactor, which he would overload by either shooting a rocket or throwing a grenade into. Then it's a mad dash to the last shuttle as the Death Star explodes around him. He escapes in the nick of time and the Death Star explodes, killing all the Imperials and Flood.