Right, this is it, then. You've reached the end. Enter and kill the two Skaarj. Find some high ground to avoid the Pupae, and kill them all.

Once they're dead, the big bad Skaarj Queen will appear in the centre of the room. Before she launches projectiles at you, she'll rear back and scream - this is when you should attack.

Also circle strafe at all times, and use the eightball's lock-on facility from the upper level.