As you arrive and ride the elevator back up you'll discover a pack of Hoppers taking advantage of the Pirate's absence. Clear the hostiles out and head back toward the Temple Access chamber. Watch out for a lone Pirate Shield Trooper hiding at out the base of the Gelbug-filled tunnel, shoot a number of the bugs to send them bouncing about, one or two may explode and take the Pirate with them (try to scan the target first but don't worry if it incinerates too quickly).
Once back in the Gel Cavern, you may remember spotting a Fuel Gel spout constantly pouring liquid. Now with your Ice Missiles you can freeze these spouts for easier transit, but for now we'll head back toward the Gel Hall chamber (save your game along the way). Once there, clear out the Gel Puffers, then leap down atop the platform which contained a Missile Expansion earlier. See the tunnel leading around the corner through the southern wall? Use your Ice Missiles to create stepping stones to reach Missile BR.06 hiding around the corner.
Once you're clear, use more Ice Missile to reach the white blast-shielded door on the northern side of the chamber. Dismantle the shield (don't forget to scan it first) and step inside to discover a narrow tunnel possessing a rather nasty-looking chasm filled with rotating gears. See the inactive Grapple Point high up on the overhanging pod? Shoot the red switch to extend the Grapple Point and swing across. Shoot the red switches on the next two pods as you swing over the chasm to extend more Grapple Points to clear it safely.
Beyond here you'll find yourself back in the Gel Refinery Site atop an overlooking platform. Turn right as you enter, see the thin support pipes blocking your path? Simply grapple them off to access Missile Expansion BR.07 ahead and drop a large pipe down to the floor, giving yourself a handy slope to easily climb up. With this shortcut created, backtrack to the Gel Hall and travel to the Gel Cavern. Move over to the unyielding Fuel Gel spout and freeze it with an Ice Missile. Leap over the pool to discover a stone head on the wall beyond containing a narrow opening.
If you check your map you'll see a large arrow pointing away from this room, whenever you see these they represent shortcuts or transit areas to other parts of the region. So activate the Morph Ball and jump in to find yourself quickly sent back to the Imperial Hall (and rewarded with a Friend Voucher for the shortcut discovery). Watch out for dive-bombing Shriekbats as you stand up, try to finish scanning one for your Logbook if you haven't already.
Cross the corridor and return to the Fiery Airdock. Scan Rundas' ship as you step towards your own for a sad observation, then climb aboard the gunship and travel back to the Cliffside Airdock (remember the Fuel Gel spouts way back in the Falls of Fire chasm beyond the crashed Federation frigate? That's our target location now).
Touch down and head for the Gateway chamber. Once there, we'll take a slight detour before moving onward to the crashed frigate. Travel to the Grand Court (where the huge stone Golem lies on the canyon floor) and use the Grapple Points there to search for a white blast-shielded door hidden along the canyon. Dismantle the shield with a single Ice Missile and step inside to locate Missile Expansion BR.08 hiding in a partially collapsed chamber - also home to a pair of docile Geemers (scan one for your Logbook).
With your latest expansion tucked away, step back outside to the Grand Court and see if you can freeze one of the Reptilicus hostiles just after it hurls a chakram at you to score the Icy Reptilicide Friend Voucher. Return to the Gateway and travel to the crashed Federation frigate. Since your arrival here you've no doubt heard from Aurora 242 by now - an abandoned Federation landing site has been discovered (surely they would've already known about it?) and within lies the means to upgrade your ship's arsenal.
Once aboard the crashed vessel step through to the Falls of Fire chasm beyond. This time there's no simple turning back. Clear the hazardous Gel Puffers before sending an Ice Missile into the first Fuel Gel spout. With your frozen stepping stone ready, leap across and freeze the second spout. Clear the chasm to discover a large stone Golem waiting patiently at the end of a short hallway.
That Bomb Slot on its chest is far too obvious to miss, so simply activate the Morph Ball and lay a bomb within it to restore power to your stocky assistant. Watch as the Golem springs to life, promptly demolishes the stone wall behind it and leaps down an enormous shaft. As the unit powers down and drops you off, stand up and take a look at the shimmering green wall surfaces above the Golem (guess what those are?) - remember this interesting sighting for now.
Dismantle the white blast shield holding you here and step through the exit. Ready for another awe-inspiring sight? The Hidden Court region lies beyond - home to a massive Golem held in place by four thick vines. Take a quick look around, one side of the region houses a huge inactive Fuel Gel pump, while an ornate wall adorns the opposite side.
Before taking in your surroundings you'll find a pair of Warp Hounds leaping down to give you trouble. Deal with both pests (use Hypermode to speed things up). For now there's not much you can do with all that machinery left behind by the Federation, but that Golem is another story. See the small Bomb Slot set in the control unit near the Golem's feet? Jump in and lay a bomb to restore power to the massive behemoth. The Golem tries in vein to break free from its shackles, but only manages to slightly damage a coverplate over one of the vines.
Stand up and step towards the cable in question. See the glowing Fuel Gel crystals the vines grow from? Scan them to learn that a constant flow of Fuel Gel is supplying the vines with energy - and is quite handily combustible. Send a single Missile into the core to effortlessly breach the vine and free the Golem's foot. Only three vines left to cut.
Step back towards the entrance of the Hidden Court and use your Scan Visor to find a weakened rock wall covering one of the vines. Use a Missile to break through, revealing a cozy alcove housing the vine's core. Use another Missile to breach this vine and free the Golem's right arm. The vine holding the left arm in place is a cinch, simply ignite the Fuel Gel spout pouring dangerously close to the vine.
The final vine won't be so easy. See the narrow tunnels eroded into the canyon wall near the vine? (where the Fuel Gel spout pours the liquid into a small pool and a swarm of Nightbarbs periodically take flight from). Freeze the dangerous flow of Fuel Gel with a single Ice Missile, then activate the Morph Ball and climb into the tunnels. Follow the path to eventually find yourself tucked into a narrow dead-end where the vine grows from. Lay a bomb to breach the core and release the final vine.
Climb back outdoors and head for the Golem's control unit. Simply lay another bomb inside the Bomb Slot to bring the Golem back to life. Watch as it happily lifts the control unit from the stone floor and inserts it into the elaborate wall - revealing an exit deep below the chamber. Climb down and head towards the visible door deep underground.
As you step towards the door Aurora 242 chimes in, this time offering an apology - the integration of the PED Suit has unknowingly allowed the unique Phazon in Samus' body to climb to critical levels (Corrupt Hypermode) - good to hear the giant brain has a heart too. 242 stresses the point that Dark Samus can't be fought without the PED, so you'll need to bear the dangers of using the system.
Step through the exit to locate the Ruined Shrine - a towering shaft decorated with a number of Golem-inspired statues. Before seeking a way to ascend the shaft, climb down to the base and look for the remains of a Golem's arm. See the small cracks lining the arm? Crack it open with a bomb to locate Energy Tank BR.03 tucked inside.
Now to climb this elaborate chamber. Leap back up to the entrance and look for a small odd yellow structure near the left Golem's head. Scan the object to reveal it as a Gragnol Hive, quickly deliver a Missile to stop the bugs spewing forth. Look up at the right Golem's load - scan the structure to learn that it's on the verge of collapse. See the large crystallized Fuel Gel spikes at the base of the statue? Send a Missile into it and watch as the entire structure collapses forward, revealing a handy Grapple Point.
Swing across to the opposite ledge and ascend the shaft as far as you can from there (deal with a second Grangnol Hive before it ejects too many bugs). Look up at the statue section high on the left wall - see the pair of thin cables wrapped around it? Follow the cables down to their bases, resting at each lies a cluster of crystallized Fuel Gel. Simply detonate both formations with a Missile each to release both cables and send the huge pillar cascading down across the chamber.
With a second Grapple Point revealed, use it to swing across the gap. Climb up the twisting ancient corridor beyond to find yourself at the base of the now-fallen pillar. Climb across the pillar and deal with the third and final Gragnol Hive on the wall up ahead. See the blockage at the top of the pillar? Use another Missile to break it loose and find an odd sight beyond.
You've broken through into what is unmistakably a Galactic Federation facility, hence the radical change in environment. The small chamber before you is littered with GF handheld weaponry, scan one of the firearms to learn that this weapons cache hasn't been touched for some time (no kidding). Step through the lone door to find yourself right where you need to be - the Federation Hangar Bay.
Take in the sights around you: a giant open hangar bay door awaits your ship above, while a large upgrade station lies below on the landing pad. Sunlight streaks through a collapsed roof section - this place has certainly seen better days. Time to get to work. Step towards either the upgrade station's terminal or the lift in the corner of the hangar to receive a nasty surprise - a female computer voice announces the arrival of hostile forces and immediate security lockdown.
Those hostiles comprise of a pair of Warp Hounds and a pack of Reptilicus Hunters. Deal with the hounds quickly and focus on their leaders (try to freeze a distant Reptilicus Hunter as it deploys its chakram if you haven't already for a bonus Friend Voucher). Break open any of the Federation crates or the Kashh pants growing on the walls for refills if the need arises. Secure the area to find yourself safely alone again. You'll have noticed the hangar bay door sealing itself as your foes approached, so we'll need to find a way to open it up again to summon your gunship.
Step towards the missile rack upgrade terminal and raise the upgrade station (even though your ship's not present, you'll need it as a handy platform). See the lift in the corner of the chamber? Restore power via the nearby hand scanner and step into the hologram. Leap over to the thoroughly ruined balcony and take a look at the right wall. See the wind blowing through a pair of grates? We'll take a short detour here. Blow the grate covers off with Morph Ball bombs and leap into the grate on the right.
You'll be promptly sucked into the pipe and deposited in an overarching command station above. See the device plugged into the wall? Scan the object to reveal it as an Energy Cell (or ZPM if you prefer...). This one is Energy Cell #2. Remember the one you recovered from a thieving groups of Pirates aboard the Olympus? You'll be locating a number of these throughout your travels, eventually you'll discover their true purpose. Step towards the Energy Cell and press A to interact with it. Follow the instructions to extract the device and take it with you.
Normally when you extract an Energy Cell, whatever systems it powered won't be so operational anymore. In this case a large energy shield blocking access to an orange door will disengage below (don't forget to scan the orange door for your Logbook). Climb into the second grate to find yourself back down on the ruined balcony. Now let's find a way to open the hangar bay door.
Leap across atop the missile rack upgrade station and hop up to the visible Grab Ledge. Once aboard the central upgrade interface, quickly dispatch the pair of Gragnol Hives nearby (one ahead and one behind you). Look around to the eastern wall, see the C-icon appearing over a narrow platform? Use the Grapple Lasso to extend the platform as a handy ledge. Leap across and peer through the large blue windows here, see the trio of Stiletto fighters in storage? The Federation sure had a good setup going here.
Leap across to the higher platform over in the south-eastern corner, then jump back atop the central missile rack upgrade arm. From here, jump across to the platform in the north-western corner with ease. Enter the narrow tunnel thanks to the Morph Ball to finally locate the hangar door's manual control override switch inside a command station. Tilt the Wiimote up and down as per the on-screen instructions to unseal the hangar door and grant your ship an entrance.
Almost there now. Climb back outside and return to the base of the chamber. Retract the missile racks into the floor first, summon your ship, then simply press the central switch on the upgrade terminal to grant your ship the hardy Ship Missile upgrade. Congratulations! Now you have the means to finally dismantle the pair of Leviathan shield generators. Climb aboard your ship and save your game before heading for the Fiery Airdock - we'll take out the generator beyond the Temple of Bryyo first.