Two plot holes in the first game still annoy me.
1) I'm still floored that stealing a Covenant Drop ship at the end of Truth and Reconciliation wasn't a major plot point in the game. They've just stolen an enemy ship. What to do with it? Can they get intel from the com channels? Use it for covert movement around the ring? But it never shows up again after that mission; it's just forgotten.
2) It's never explained where Keyes is going. Early in The Silent Cartographer, he says "we're still on route to the objective" - but doesn't say what it is. At the end of Assault on the Control Room, Cortana is talking about needing to stop Captain Keyes.
CORTANA: The Captain, we've got to stop the Captain!
MASTER CHIEF: Keyes? What do we-
CORTANA: The weapons cache he's looking for, it's not really-we can't let him get inside!
It's implied around the edges, but I wish they had explained what it was Keyes thought he was searching for, why, and how they determined to go there. I was so confused my first time through. Wait where's he going? Then later, he went to weapons cache? Wha?