The Old Tribes

Move through the first door here and start sniping away at the distant Hunters, ducking behind one of the walls to use as strafing cover. When you're done, open the nearby door, then use spiritwalking to avoid the security tripwires; walk along the path and activate the security panel to disable the tripwires. Return to your body, then walk to the end of the hall (avoiding the door on your right for the moment) and head through the door there. If you don't annoy the slaves, you can receive a large health boost here, as well as your choice of either lightning or fire ammo for your Leech Gun. If you head through the portal nearby, you can also spiritwalk up the ramp to receive some extra ammo.

With all that done, return to the tripwire room and head out the other door, using the panel nearby to activate the walkway over the gap. Enemies will, of course, start to spawn during your traversal, so be sure to pop them as they appear. You'll have to move in and out of this large room a couple more times, so you can't really afford to let any enemies live. Just fire at them as they pop up and move on.

More Tripwires

After moving across the walkway, bust out your spiritwalking and disable the tripwires in the first corridor, then repeat the process on the next one you enter. Again, there'll be two doors here, so head to the end of the hall and activate the portal there to step through; you'll be in the sniper roost you probably cleared earlier on. Use the switch here to activate a distant walkway, then take out any of the snipers that spawn in, if possible. With that done, return to the tripwired hallway, spiritwalk through the gate to shut it down, then spiritwalk across the gap here to activate the walkway on the far side of the gap.

You can spiritwalk through most of these rooms to reach the tripwire shut-off switches.

After crossing the walkway, disable the tripwires in the far hall, then start climbing the walkway at the end of the corridor; it'll lead you to a platform higher up, from which you can pipewalk until you're over the small catwalk that stretches from one side of the room to the other. Drop down and run like the dickens, and you should be able to activate the portal and escape without taking much damage from the enemies that warp in.

Shuttletastic!

After killing the hunter on the far side of the door, use the shuttle and glide a few rooms away until you find another dock, then land. From here, you'll have to avoid the sniper fire while spiritwalking up the ramps available to you. When you do so, you'll be able to kill the snipers, and activate the panel at the top of the ramp, which will open a passageway in the ceiling to you. Hop back in your shuttle and glide up, watching out for more of those floating mines.

When you reach the next large area, note that there are four landing platforms, but that only two of them will actually lead to an uncovered dome. Your first goal will be to kill all of the enemies, since you'll need to move around in this room a bit. Your primary objective, however, is to disable the fan in the ceiling and move on. To do so, you'll need to activate two switches at most of the platforms: one to disable the forcefield (use spiritwalking to reach these switches) and one to expose the radioactive core of the power conduit. Some of the platforms will have one or both of these switches already active.

Pull the energy cores out of their housings to unlock the path leading on.

Basically, when you land at a platform and disable both the forcefield and the shielding, you'll be able to shoot the shielding off of the core, then use your shuttle's tractor beam to drag the power core out of the housing; it'll be a bright blue object. Just lock onto them with your tractor beam and drop them after dragging them out; you don't need to do anything special with them.

When all four cores have been pulled out of their housings, you'll be able to move through the fan in the ceiling and proceed on up to the next guiding fire up there. You'll eventually come to a secret Hidden Citadel. To enter, use your tractor beam to pull away the four pieces of debris in front of the locked door, which will then automatically open.

When you enter the Hidden base, you'll encounter Elouit for the first time. She's the leader of The Hidden, and offers you a deal: find and kill the Keeper, and she'll open a portal back to Earth for you, Jen, and the rest of the refugees on the ship. It's a tall order, but you haven't encountered anything that'll stop you yet, so you might as well take her up on it.