Hidden Agenda

Make your way through the biolabs, using your spiritwalking and alien hand to bypass any hazards. After you spot the Keeper, you'll soon see an Acid Gun suspended in midair. To obtain it, head into the two side rooms here and shoot the white power cells within; be sure to obtain any ammo or health inside the rooms first, then retreat to the doorway before shooting the cells, or you'll set off tripwires.

After obtaining the Acid Gun, use it to kill the Hunters that start spawning in. It's essentially a shotgun, so get up close and personal before firing it at your targets. The alt-fire will pretty much instantly kill anything it hits, but it uses a lot of ammo and has a long reload time, so avoid using it except in emergencies. When enough Hunters have spawned, you'll be able to pass through a portal to get an update on Jen. She's apparently being tortured! Dastardly!

Move through the next room, using your alien hand to unlock the forcefield, until you come to another room with Hunters and a turret that's firing on you. The forcefield here will be spiritwalkable, but there's no where to go at the moment. In order to move on, you'll need to park your body in the small green chamber near the forcefield, then activate the switch here twice; you're essentially activating a horizontal elevator that'll move your character around in an axis. As mentioned, two flips of the switch will get you to an area with a portal that'll let you move on; if you hit it three times you'll be able to use another broken video poker machine, which apparently dispenses some ammo if you use it a few times. Regardless, the portal is your key to exiting this little maze.

A Situation of Some Gravity

After exiting the portal, bypass the Slaves and move on through the crawlspace at the end of the corridor to encounter more robotic flyers. Kill them, then spiritwalk to disable the forcefields before moving up the walkway. After passing down the central walkway and exiting the crawlspace beyond, you'll find yourself in a room with a lot of pipes and a few gravity switchers.

This situation looks complicated, but it's not incredibly so. If you look in front of you, you should see two gravity switches, not including the one you're standing on. One will be on a "wall", and one will be on the "ceiling", a bit further away. You need to get as close as you can to the one on the ceiling, then activate it, as there's a crawlspace nearby leading to the second half of this room. It's best to do so by first shooting the portal on the wall, hopping over the pipes to your left, then walking down to the portal on the ceiling and shooting it, which will let you get through the crawlspace.

After crawling through, walk a bit until you see a forcefield and another gravity switch on the ceiling. Hit the switch when you're standing above the forcefield, and you should fall directly onto it. You won't go through, but if you spiritwalk, you'll drop down next to a switch, allowing you to open a portal. From there, find another switch on the wall, and you should be able to get close enough to the portal to jump through it from the ground, unless you want to stick around and play with more switches to find some semi-hidden ammo.

More Fliers

After seeing the Keeper warp away again (he's going to be tough to get a handle on), find the broken section of the floor and drop down. Get ready for a fight against some flying opponents here, as a few Drones will pop out of the walls and attack. Kill them all, then move through the portal that opens to move on.

Jen

Move ahead here until you find a barrier, then spiritwalk through it. It's easy to miss the code for the keypad here, since it's written on the floor: 2432. It's also difficult to put it into the keypad while you're still in spiritwalking mode, due to the fuzziness of your view. Just keep in mind that the number in the upper left corner of the pad is actually 0, not 1, so the sequence goes from 0-7 instead of 1-8.

After disabling the forcefields, crawl through the red crawlspace nearby for ammo and a heal, then crawl through the crawlspace near Jen. You can get some Leech Gun ammo from the door to your right, but the path onwards is through the door to the left, under the turret.

It'll lead you into the Surgery Control Room, where the Sphere's mad doctors are constructing Mutates. Mutates are former humans that have been converted by the Sphere into horrific defenders, possessing decent speed and a huge claw to impale you with. Needless to say, keep your distance and fire at them with a rapid-fire weapon. If you think you can tag them with an Acid Gun alt-fire shot, then that would be ideal, but they'll usually be moving too quickly for such chicanery, making a red-ammo Leech Gun or Auto Cannon attack preferable. You'll need to take down two Mutates, then two Hounds before you can escape this area. If you find yourself getting killed by the Hounds, check out the holes from which they appear and use your Crawlers in proximity mode to mine the entrances when you reload your game.

Spiritwalking

When you pass through the next door, spiritwalk through the forcefield on your right and crawl into the hole there. You'll eventually pop up into another room and be able to unlock the door that prevents your physical body from moving on. Do so, then walk up to the switch by the window; it controls a shiftable portal. You want to move the portal so that you can walk through it with your body and into the next room, then spiritwalk back through the portal and flip the switch again so that the portal shifts over into the room across from the window. If you do so, you can return to your body and walk back through the portal to move on.

After passing through another couple of portals, you'll come to another surgery room. This one contains four Mutates, and sadly enough, they'll come out at certain times, regardless of whether or not you've killed the previous one. If you waste too much time here, then you'll possibly be facing off against four enemies at once, which is a Bad Thing. It's best to start off by sucking up the lightning ammo for the Leech Gun and using that to quickly dispatch the first couple of Mutates, then spamming the remaining two with the fire ammo from the other leech station to finish them off, ducking and weaving all the while. When everything's dead, a portal will drop from the ceiling, which leads you to Jen. Use the switch near her prison to free her. Her awful voice acting comes along for free!

After you get the voice message from Elouit, check the blue doors for ammo and health, then head through the portal to end the level.