Cliffside Airdock

After landing, head back to the Grand Hall where the large statue covered the ground. Use the grappling point and turn yourself so that you can jump onto the small ledge to your left with the white door. Destroy it to find a Missile Expansion.

With that done, return to the crash site and start heading through the ship. Use your missiles to freeze the flow of fuel and jump across. The labor golem there can be activated in bomb form, and will drop you down to the Hidden Court, where a war golem lies chained. Defeat the Warp Hounds to begin some puzzle solving.

Set My People Free

The war golem needs to be activated, but can only move when the four vines that bind him are severed. You can disconnect one of the hand vines by charge-blasting the jet of fuel that comes out of the wall here. The other hand can be disconnected by using a missile on the weakened wall that it protrudes from; jump to the hole that's created and use another missile on the base of the vine.

You'll need to set this golem free to move on.

Roll up and fall into the small control light in front of the golem and use a bomb to feed him energy. That'll charge the panel off one of the foot vines, allowing you to missile that one as well. The last foot vine requires some trickery. See the pool of lava near the golem? And the lava flow that goes into it? Hit the flow with an ice missile to freeze it, then roll up into the ball passage nearby and move over the frozen lava. Navigate the path until you find another vine root and blow it with a bomb before returning to the main room here. With all of the vines uncovered, you can drop back into the power chamber and activate the war golem, which will open access to the Ruined Shrine.

The Ruined Shrine

First things first: drop to the bottom of this cylinder and blast the weak spot on the golem fragment to find an Energy Tank. Return to the middle platform and hit the crystals to your right with a missile to drop a grapple point. Swing across and start climbing the platforms that lead upward. Eventually you'll come to another stopping point: fire your missiles at the crystals on the platform across the way, and you'll start a chain reaction that will cause another platform to drop. Swing across and move around to where you can reach the platform. Destroy the barricade with missiles and move on into the Federation Landing Site.

Nab the energy tank at the bottom of the pit here.

Inside the site, you'll have to deal with an enemy ambush of Reptilizoids and Warp Hounds. Kill them, then start exploring.

Unlocking The Doors

In order to land your ship and upgrade it, you'll have to manually unlock the bay doors that float overhead. First, find the elevator in the corner and go up. There are a couple of ventings nearby. Roll up under the white one and lay a bomb in front of it in midair to unlock it, then bomb yourself up and through. You'll find an Energy Cell in the room beyond, so grab it and return down via the vents.

Next, use the access panel on the ground here to raise the platform back up from its retracted state. Hop up on the elevator again and use the grab ledge to jump to the top, then scan and use the grapple to pull out the nearby ledge. Jump from there to the uppermost part of the platform, then jump to the corner platform and roll up into a ball to access the control room here. Using the mechanism inside will open the bay doors.

Now your ship has missiles and can perform bombing runs on specific targets.

Drop down to the ground floor here again and retract the platform at the control panel, then flip to the command visor and scan the landing icon to summon your ship. Pressing the control panel again when the ship is landed will upgrade it with missiles, allowing you to summon bombing runs on special targets. Nice! Now that you have that done, get into the ship and head to the Thorn Jungle.

Thorn Jungle

When you reach the ship, head to the Thorn Jungle landing pad. Proceed down the path in front of you and you'll find Space Pirates, but these guys can enter Hypermode themselves. Fight fire with fire and use Hypermode to kill the both of them. While in Hypermode, you can also destroy some of the growths on the ceiling and the walls. Destroy everything you see, and you'll unlock a small passage leading to a missile door. Go through to find an Energy Tank.

Return to the hallway. There should be another smashable panel in the ceiling. Destroy it, then jump up and roll through the passage there to find the power to the shield by the door. Shut it down, then return and head through the door here. The Pirates on the other side can apparently start a Phazon Overload in your suit, so be careful around them.

Bombing Run

When you reach the jamming signal near the Pirates, you'll have to scan it. If you do so, you'll find a switch on it that you can grapple. Grapple it and pull it to shut off the jamming transmission, then switch to your Command Visor and have your ship come down for a bombing run on the huge door here.

After that happens, a Berserker Knight will appear with Pirates to help him. The Pirates are annoyances here, so keep an eye on the Knight and fire at his Phazon balls that he'll throw at you. Eventually you'll crack his carapace and will be able to fire on his pink, exposed brains to finish him off.