After you acquire the Super Missile ability in Ghavoran, you are able to reach a shuttle to the area of Elun.
Get a Missile Tank
Go to the right, open the door, and go through. You will reach a save room. Save the game if you wish, then go through the door on the right. There will be a cutscene.
After the cutscene, go to the right to reach the next room. Use a bomb on the floor near the green door to break open the small room below, then go down into the small room and use multiple bombs on the left side of the floor to open a path. Roll into the Morph Ball Launcher on the left and use a bomb to activate it. At the end, shoot the red thing in the ceiling to open the path. Jump up from there. You can't open the door on the right yet, so make your way upward through the room. There is an Ammo Recharge Station on the way. Go to the upper right of the area and go through the door there.
There will be a cutscene. You can wait for the creature to flash and perform a Melee Counter. You will absorb the X parasite. Yellow X parasites restore energy, green restores missiles, orange restores ammo, and red restores energy and ammo by a large amount.
Go downward, and if there is a flamethrowing creature blocking your path to the left, kill it, then go to the left and use a bomb on the floor to break open a path. Go downward and kill the ceiling creature, then go through the door on the right.
There is a tunnel at the upper right that leads to an Energy Recharge Station. If you use it, go back through the tunnel afterward to return to the room with the fan. Drop down to where the fan is blowing. Drop down from there and kill the creature, then go downward and kill the eyeball creature, then go down to the bottom and kill the creature there. If you want a Missile Tank, go back up to the fan and Speed Boost toward it, then ready a Shinespark. Before the purple Shinespark energy wears off, quickly go downward, sliding through two tunnels, until you have slid through the second tunnel. Go to the left wall and press B to Shinespark upward and destroy the Speed Booster Blocks above you, revealing a hidden Missile Tank.
Get an Item Sphere
From the area below the second tunnel that you slid through, shoot the upper right block of the wall of the dead end to reveal a tunnel. Roll through it to reach the next room. Roll into the Morph Ball Launcher and drop a bomb to activate it. Then shoot a missile at the door on the right, then open it and go through.
Shoot at the right side of the ceiling to open a path. Shoot the item sphere that the statue is holding, and jump onto it to get the Plasma Beam. It replaces your normal beam, so just use it the same way: press Y. It is stronger than your previous beam and can shoot through glowing green barriers on doors.
Reach the Next Area
Go to the left and shoot a normal shot at the door on the left to open it. Go through.
Go upward through this room and go through the door at the upper right. Then go to the right and shoot the door on the right to destroy the Plasma Beam Cover. Go through.
Kill the fire-breathing creatures if they get in your way, then go to the blue wall at the upper right. Climb up it and kill the small eyeball creature if it gets in your way, then at the top, jump onto the ledge on the left. Go to the left side and slide through the tunnel, then kill the eyeball creature on the door and go through. There will be a cutscene, then a battle will ensue.
When the soldier spins its spear, jump and do one or two Flash Shifts to go to its other side. When it jumps onto the wall, move left or right to prevent it from landing on you when it jumps off of the wall.
Eventually there will be a cutscene and the soldier will change form. Continue doing Flash Shifts to get behind it when it spins its spear. Whenever it jumps onto the wall and then drops downward, two black waves will shoot out from its sides after it lands on the floor, so be sure to jump to avoid this.
Eventually, the camera angle will change, and the soldier will reach back its spear. Do a Melee Counter when you see the flash, then do a second Melee Counter after the second flash. Then the battle will end.
Get an Energy Tank
Go through the door on the left. Shoot the upper left ceiling to break open a hole, then roll into the tunnel there and use a bomb to reach the Energy Tank.
Return to Ghavoran
From the tunnel where you got the Energy Tank, use bombs to break open the floor if necessary, then at the bottom left of the room, shoot open the door and go through. There will be a cutscene. Afterward, Speed Boost to the left to kill the creature along the way, and go through the door on the left, then save the game if you wish. Go through the door on the left and step on the glowing panel to board the shuttle back to Ghavoran. There will be a cutscene. The E.M.M.I.s are now active again.