At the end of the Truth and Reconciliation, when you get to the docking bay with Captain Keyes you will meet a whole slew of Covenant waiting for you. Go strait to the controll panel-that you would normally hit when the battle was over-and hit "X". Then fight normally.

If that reckless Keyes gets killed, it will show his corpse, then go to the cut-scene of you activating the control panel, then the screen goes white, and you go strait to the next level.

You can also kill Keyes yourself just to end the level early.