You begin in a corridor with several sealed doors and a couple side rooms with consoles. At the far end, one door is open. Go that way to a very large courtyard with a big structure in the center. Including the way you came from, there are four doorways leading to side areas. If you look above them you'll see they're numbered by placards, 1 through 4 in a clockwise order beginning with the doorway you came from. The other three are blocked by forcefields. Behind the forcefield of Door 4 you'll see the supertank guardian Rsaoi: your first boss-enemy encounter in the game. Defeating Rsaoi will be your last major task in the defense base and surface areas of the Citadel.
Forcefield 1[edit]
The main objective before defeating Rsaoi will be to get these forcefields down. First, have fun shooting the radars--that is, if you like watching the reflectors bounce around everywhere (and who doesn't?). Jump up onto the Mazrium platforms circling the courtyard. You can reach them either from the broken column or the sloped part sticking out from the center structure by Doors 2 and 3. Look for a vent high on the wall near Door 1, and jump to it. Follow the air duct to a room with a power conduit (there are missiles in that side duct to the left) and shoot the conduit to disable Forcefield 1, which is blocking Door 2, and release the doors in the corridor where you started the level. Take a look at the now-opened storeroom next to where you entered the level, where there's assorted ammo. Go around to the far side of the stack of crates, and shoot at them to find a secret area within the stack with lots of missiles. You'll need these later.
Forcefield 2[edit]
Go to Door 2 now. The door on the left inside has a magnetic lock like the others; go inside the right-side door where you'll find a remote-control station overlooking a chamber with a power conduit. Use the remote control, which activates an HSD in a network of air ducts. Explore the ducts. At one point you'll see a set of trip-beams with a teleporter just visible past them. When the HSD crosses these, you'll feel "a slight draft behind you." Switch from the remote right away and turn around: the wall behind you has opened, and a gun turret inside will start shooting you in the back. There's a nice stash of items inside as compensation. When you've taken care of that interruption, take the HSD through the teleporter and follow the duct to the chamber with the power conduit. Destroy the conduit to disable Forcefield 2, which is blocking Door 3 and unlocks the door outside. This also drops the forcefield in that other entrance to the chamber (the HSD can't fit through here and will be stuck in the chamber), disables the "beams of lethal intensity" and opens a door here in the control room which leads to the network of ducts.
Take a minute to go through the ducts: there are lots of items. A little ways inside is an irregular dark patch on the wall, with a secret area inside. Both areas where the "beams of lethal intensity" were are also counted as secrets. Past the other set of trip-beams is a dead-end area with ammo. When you leave here, watch out! You've triggered a trap which placed a string of mines down the duct. You can avoid these by keeping to the wall, then when you're safely past, shoot a scattering weapon like your #6 at them to destroy them. (You can also trip this beforehand with the HSD, if you didn't already.) There's a Li'l Buddy and a full-health in the chamber. Finally, the unsealed door outside the control room goes to a small storeroom with ammo.
Forcefield 3[edit]
Go now to Door 3. Inside is a deep chamber with that red waste stuff at the bottom and a bunch of fixed and moving floating platforms you'll need to jump to and from. Down near the bottom is a door you'll need to get to. This is one of the more difficult parts of the game, because of how the 2.5D nature limits how much you can look up and down. You'll probably need several tries to do this. If you fall, there's a teleporter at the bottom of the column to get out with. There are a lot of items in and around here, including an Invulnerable floating in the air next to the column.
Jump down to the platforms and look for a shootable switch on the outer wall about halfway down the chamber. This unlocks the door and activates a Mazrium platform going down to the door. Inside is a power conduit: destroy it to disable the forcefield inside Door 4. From now on the teleporter on the column will lead into here instead of up top like before (how mean!). You'll hear an intermittent sound a bit like a vacuum cleaner that wasn't there before. This is Rsaoi outside: get ready for battle!
Big boss[edit]
Rsaoi isn't too difficult to dispatch: about 25 missiles will do it. Those red discs that bounce off the walls can be a bit of a pain. Just keep strafing to keep from getting hit by the whole string of them that are fired at once, and don't worry if a few bounce back around and hit you in the back. With all the full-health throughout the level you shouldn't have a problem if you run low.
After defeating Rsaoi, the big door inside Door 4 is powered up, and leads to a big storeroom. The level exit is in here. Also there's a side room overlooking the storeroom, with a (most likely) non-working teleporter. This goes to a secret room with an assortment of items. (If you look on the automap you'll see that the broken-down part used to be a corridor between here and the overlook-room.) If the teleporter isn't working, go back to the red-waste chamber and jump down to the bottom. On the column, on the opposite side as the teleporter, is a shootable switch, which activates the secret-area teleporter in the overlook-room. (If you fell down there earlier, you probably shot the switch then, not realizing what it was for.)
You've now completed this phase of your mission. You'll want to go around and gather missiles and stuff. If you used missiles on Rsaoi there should be enough or almost enough to resupply completely if you didn't use them for other things. After you've stocked up, exit the level and proceed to the factory area.