At this point you've found the Captain, and he's part of the flood. You get his info anyway. Now you have to get back to the shuttle bay. First defend your position with grenades until you can get out. There might still be a medic kit over to the left to use. Now go straight, right, and left, and watch them fight for a while. You'll then be back at the shuttle bay. Run and jump onto one of the two arms of the ship that's there. You can jump to it without harm (well run and fall really). Now jump to the middle area. Don't even bother fighting the guys below. Just jump from there to the banshees, because once you get into one, the level is over.

Master Halo Walkthrough