After landing at the Fiery Airdock, head through Imperial Hall and Gel Refinery Site until your in another Morph Ball area. Let the critters take you all the way to the top and you'll find a tunnel that leads to more missiles. Now let them take to you to the lower path in Main Lift, towards the missile door. Keep moving through the halls towards the Gel Processing Site. Ignite the fuel stores next to the Morph Ball panels to make the center platform rise. Keep doing this to make it rise to its highest point (remember - scan everything and fuel gel will ignite if shot).
At the top, in the Gel Hall, hit the gel-spewing face right as it's passing the dangling yellow cord. The resultant fire blast will shred the cord, lowering a platform for safe lava stepping. It also happens to contain another missile upgrade. Keep moving forward and you'll come to the next boss battle - Rundas, your fellow hunter.
For an ace bounty hunter, Rundas falls pretty easily. Just keep pounding him with charge blasts and the occasional missile to stun him, yank the armor off and then go all out with the Hyper Beam. He's done in no time, and now you've obtained the Ice Missiles. If you need an energy boost during the fight, just shoot any of the ice packs he throws your way. The next room is traversed by priming the fuel pump, then freezing the flow with the Ice Missiles. This is a trick you'll use often in the game. Too bad there's nothing you can do here yet, as the shield generator requires some heavy duty weaponry to fell. Time to head back to the first landing site - do this via the Gel Hall into the Ice Door-covered Gel Purification Site and you'll find a new missile upgrade and shortcut to the Gel Refinery Site. Now back to your ship, and back to the G.F.S. Theseus, where you first activated the uplink. Head through the Falls of Fire with your new Ice Missiles and you'll come across a fully functional golem who'll take you for a quick ride to the next point of interest - Hidden Court.
Just follow our lead and you'll be fine.
The next point of interest is the bottom of the Ruined Shrine. The broken chunk of golem is hiding an Energy Tank, so please, grab it. Then blast your way up the shrine into the next room (consider the yellow rocks powder kegs and you'll do fine), and your ship will gain the ability to fire missiles. First you gotta clear the room, ride the elevator up and slide up the Morph tunnel into the room with an Energy Cell. Once removed, it lowers the shield blocking the orange door.
Continue up the room to open the hangar door. Now you can call your ship in, raise the upgrade platform via the nearby touch switch, and presto - you've got the ability to call in air strikes. First one of the day is all the way back at Temple of Bryyo. There you'll have to deactivate two jamming dishes before you can call the ship - also be aware of new enemy scans. You are scanning everything still, right? Your second air strike is at the nearby Temple Generator room, where you were gazing upon the shield generator earlier. Call in the ship, bust up the shield and you're off. Take the Morph Ball shortcut in Gel Cavern back to the Imperial Hall and fly to the Thorn Jungle Airdock.