That. The flood would still be in the feral stage at this point so without any central hivemind it probably mindlessly infected everyone aboard the ship. Unless, of course, they formed a gravemind before infecting everyone. A stretch, but most of them are probably dead. A gravemind might have had the forethought to think "okay let's chill here until they make their way to a major population center." I would like to see Red alive, though. Maybe Anders in Halsey's absence. Maybe they're gonna use a seriously fucked Serina with some nano bullshit to bring back Cortana? I dunno. SERENA FOR INFINITY'S AI
We'll see what 343 wants to do with this, they're new to the flood so I'm not sure they know all of the possibilities. Then again, look at at Jun.
They have that blow-hard Roland already. If you read Escalation, the ship made it into Jirhalhanae space -and even had a flood infection form or two on board. If you read the black box entries in Halo Wars, the humans didn't'\ know how to treat the flood or deal with it. They had to quarantine about half of the ship because they didn't know what to do. Added that during the flood encounters, lots of the crew got infected and were even left behind. Added they got rid of their Shaw-Fujikawa Slipspace drive and detonated it to swallow up the planetoid and the Covenant who didn't get away quick enough, and the flood on that world with it. So they still had a quarantined ship, and loads of personnel MIA or just unaccounted for. They would have had to be in cryo for much of the Human Covenant War. Eventually I'm sure something happened if you watch the Legendary ending. Added their systems could probably only last for so long -they would have had to leave for a number of reasons, and the flood may have been one of those reasons.
So someone or something forced them to abandon ship. They may have very well perished and succumbed to old age or other causes -if the the remainder of the crew found somewhere habitable for human life. So by the time the war "ended", many of them would have a high chance of being dead. And since we know A.I. in this universe can begin and go Rampant after seven years or more. So if Cutter and company died somehow, Serena may have gone rampant and thought herself to death by the time anyone arrived on the scene.