: That was kinda lame. 'Gajat is presumably dead, the Spartans saved the day
: with very little resistance, Clayton is arrested, that whole side-mission
: with Lasky and Petra was pointless, and Spirit of Fire only makes a brief
: and hopeless appearance. Pretty weak conclusion to that whole story arc.

: Although we did get to see puppy-Clayton for a brief moment:

: So is it pretty safe to assume that SoF was lost to the Flood? Because that's
: what that ending heavily implied.

At the end of Halo Wars we see all the pods go into stasis mode. All the pod doors are open in the comic.

Additionally, there's no evidence of Flood growth on the exterior or interior of the ship, just a spore.

I'd say that this may take place after the legendary teaser in the game, and the crew may have been awoken and evacuated.