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Ok, now that I'm not a drunken mess here's my theory:
SoF wasn't lost with all hands, but recovered by ONI, quarantined and covered up. Why do I think this?
The Evolutions story Mona Lisa takes place in October 2552, on a unspecified day at the Alpha Halo debrisfield.
In the story a team of Marines infiltrates a top secret ONI facility that has been there testing the Flood as bioweapons.
Now, Halo 2 starts off at October 20th. And Alpha Halo is destroyed at September 25th. The ML arrived at the debris field shortly after the destruction of Halo, presumably within a week or so and began testing with the Flood. This seems too early when you factor in travel time for the Chief and Cortana to make it back to Earth, Mona Lisa to get there, time for recovery of samples and experiments, then the Red Horse's prep and travel time. I don't think it adds up, or at least give reason to think that the ML was there before the Chief got debriefed.
How on Earth do they know about the Flood and Halo at that point? Because Chief and Cortana aren't back on Earth to tell them about the Flood/Forerunners at that point in time. It is safe to assume the distress call from Cortana had some info about "Flood", but the question still remains: how does ONI suddenly turn up with a fully fleshed out plan to use Flood as bioweapons, and with a ship fully equipped and prepped for such an operation? That's not something that could be thrown together in the short period of time they had. Unless, they were prepared for such things and already knew about the Flood in a some way, is where SoF comes in to play, because they are the only ones who had UNSC contact with the Flood before them.
So I believe ONI somehow found them, put them in quarantine, covered the whole thing up, and then already planned for what they did during Mona Lisa. Halo is destroyed: Cortana leaves a distress beacon with information in it for the UNSC to find them. However, they capture a Covie ship and make it back to Reach (First Strike) and ONI shows up with their plan to use the Flood.