Most of the human gear I found was in corners in the hanger bay and in empty prison cells.
Could be I need to go through that level again but That's what i remember and and that would be a pretty reasonable excuse for the gear being on board as I doubt the covenant would want their captives having ammo even if they didn't have weapons.
A more important question would be, Why did the covenant take captives in the first place?
They weren't known for taking prisoners which would beg the question why have so many cells if you didn't take captives.
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