Welcome to the factory! You're done on the surface and have gone down into the depths of the Citadel, and won't be seeing the outside for the rest of the mission. Your primary mission in the factory area is to interrupt recently-resumed manufacturing by the Ioxian forces. You begin in a tall room with several transport tubes and various things stored. This part of the factory has deteriorated in many places, with broken walkways, collapsed ceilings and gaping holes in walls. Your first objective is to shut down these transport tubes. The main door up on the low platform is unpowered. The power switch is in that control overlook, but it's out of reach and you'll have to find another way there. You can use Low-Grav Boots, but the intended way is much more interesting. (Those glittery purple surfaces are probably made of refined Mazrium, and is an awesome-looking texture. You'll be seeing more of it.)
Transport Tubes[edit]
Before continuing, go over to those stacks of boxes by the level entrance, and use them to jump up to that high ledge. There's various ammo inside that room. Now, to power the door: go back out to the transport tubes and jump down the one without the grating, into the basement. (Watch out for the Droppers.) Follow the conveyor through a teleporter to another room. Just to your left is a wall you can destroy to reveal a secret storage room. (When you battled the Dropper you probably destroyed the wall as a matter of course and may not have noticed. As such, it's easy to not realize this is a secret room and pass it by.) Take the door from here back out to the main room, where you'll be up on the walkway, to the control overlook. Hit the switch to power the door.
(A technical aside: If you look on the automap you'll see that the basement the transport tube led to is off to the side. Due to limitations in the sector-based "2.5D" level format, rooms ("officially" at least) can't be above or below each other. Here, it was emulated with a teleporter in the transport tube.)
Go through the powered-up door to a room flooded with the red waste because of damage to the big tank. The lower door leads to a corridor blocked by a forcefield. Jump up to the far walkway instead. Inside the functioning door there's a disused control room, with items. Go through the broken door with the hole in it at the other end of the walkway, up the ramps, down the lift to a room with four power conduits, one of them destroyed. Destroy the other three conduits to shut down the transport tubes and complete this objective. This has also deactivated the forcefield in the corridor.
Generators[edit]
Go now to the flooded room, through the corridor and deactivated forcefied inside the lower door, to a big storage room. There's a ton of ammo and items in here. Jump from box to box and up to the Mazrium platform. (There's a Retina Enhancer on the opposite end of the room from the upper door.) Take the door on the wall to a tall flooded room with a factory that manufactures HSDs and other enemies. This room is a pain in the backside: you'll have to do long jumps between platforms, and fall into the red gunk if--errr--when you miss. First off, there's a Secret Level Access Keycard hanging in the air next to the factory on the side closest to the way you came in here. If you jump over to the corner of the room diagonally opposite the way you came in, there's a hidden door inset just slightly into the wall, with a secret area inside. There's a Big Buddy hanging in the air behind the factory near here too. Inside the door blocked by the forcefield is the level exit.
Jump over to the door to the left of where you came in, go down a big, long, descending spiral passage to several power conduits at the far end. Destroy the conduits to complete your objectives on this level. There are items all over the place along the spiral passage, behind posts and such.
Before you exit, a really nice secret area is now accessible. Go back to the first room with the transport tubes. The grating over #3 is gone now. (Note the placards above them.) Jump down this, and follow the passage with that great purple texture. In the corridor with the forcefield you probably saw the windows with the purple surfaces inside. You're inside there now. This leads to a small room with a waste tank, and items. When you're done here, head back to the factory room, jump around the factory to the door in the right-hand corner, and take the teleporter inside to exit the level.