Playing on Heroic I just dropped the "package" off to the Pelican that will take it back to the Piller of Autom.  Capt. tells you to run up into the gun and shoot down the giant covenant ship.I was so excited to finish the game I rushed by the elites not killing them.  Ran up the ladder jumped into the gun seat.  Game saves , checkpoint.  Now im getting nailed from behind , from the elites I left below and from incoming banshies.  Im getting killed very quickly.  I tried jumping off and taking care of the elites down below but time runs out , the covant ship gets too close and its game over.  A few times I quickly killed the elites and made it back to the gun but was over run by banshies.  That final part seams to be on a timer or something.  I tried for hours to get past this part but i am truly stuck.  I was so pissed I just shut the game off.  Ill have to replay the final mission.  
 
I want to know exactly what im supposed to do once in the gun.  Do I focus on the banshies and other incomming covenant or do I shoot down the giant ship?  Where do I shoot it?
 
Thanks for the help.

Giant ship rolls in somewhat slowly after getting up there, at least from what I saw (my roommate was the one controlling the cannon), so I'd think you have time to gun down a lot of the phantoms/banshees before the ship gets all the way in position.
 
Also, from what I saw, the ship only takes one shot if you shoot it in the right spot.

You don't shoot the cruiser until Keyes tells you to.  Otherwise, focus on the Banshees and Phantoms.

Your supposed to wait until the big covenant cruiser is close enough to shoot. What i did was hide on the stairs behind the gun and when the Cruiser was close enough, i quickly got in the gun and fired at the glowing red core of the Cruiser.    

I did it!  Amazing ending.  @rosebud04: I took your advice , hung out till I heard Keyes say " Now Spartan" (or something like that, the music changes, you will know when to shoot).  The last mission took me 3 and a 1/2 hours to complete, and this was my second time running through it, meaning I knew what to do and it still took me this long to beat.  Do I suck or did it take that long for any of you to finish?
 
Epic game.  ***** five stars.