Torvus Temple Super Missile Expansion Glitch
The first time you come here, you are thrown into a scripted battle.
This is how it is supposed to happen: Two Pirates Troopers swoop in on a Pirate Skiff, then jump off and attack you. After you kill them, two Pirate Aerotroopers show up. After that, four Pirate Troopers attack. Finally, after you kill the four Pirate Troopers, the Super Missile expansion shows itself and you can proceed.
What happened to me was that one of the two original troopers didn't jump off the ship--and flew up into the sky with it, removing it from combat and letting the 2 aerotroopers spawn! I killed the 2 aero and the 4 other normals... but the battle music didn't stop, the doors didn't open, and the super missile didn't spawn. Instead of resorting to my previous save, I look around and up... I see the lone trooper shooting at me from waaay away above the room--so far that his shots vanish from the distance before they even get close to me. I moved around and pinpointed the location of him outside the top and fired about 30 missiles at him until he died and the super missile spawned.
I haven't been able to repeat this beyond that one time, but it was a little depressing just looking around for it.
Found a way to duplicate this, partly. As soon as the drop ship swoops in, run right up close to it and shoot one of the pirates. Instead of jumping off, he will stay on and shoot at you. The drop ship will then fly away. However, you only need to kill the remaining pirates that show up to get the super missile upgrade.