Either doing UNSC missions or in the cryo tube.
That question always mystified me. If the Covenant were attacking Reach in force, one would expect them to put the only other hyperlethal Spartan into the field. Yet, you don't hear of any of his ordinary heroics, no Supercarriers exploded from the inside (well, one, but that was Jorge), no secret Forerunner data retrievals (well... i'm starting to notice a pattern here), no last-minute escapes of cities that are about to be completely destroyed (hah! That's new!... well.... old....) and no deaths of any Prophets in the area. Plus, at the end, you can see him just chilling in his cryo chamber in the hangar of the Pillar of Autumn, as if his presence wouldn't have changed the war. If anyone asks me, they should have added the MC to the Fall of Reach, and it might not have fallen so hard.
He was at the Battle of Reach, that I know. But what he did during said battle I have no idea.