Eradicator/Surface Base (D1)

Upon your arrival at the Citadel, you'll be in a tunnel that leads to a mechanical room inside an air vent. Shoot the vent and head out to the concourse outside. To your right you'll see a switch-activated platform that leads to an overlook that appears to lead to where those Mazrium platforms are coming from. The inside is blocked by a forcefield right now, but you can get in here later.

Base
Work your way down the concourse, which doubles back a few times and is patrolled by some LSDs (land security droids) and gun turrets, to the far end. It looks like a dead-end, but isn't: find and climb into the vent, which leads to a large room with a big platform, a door and the end of a conveyor. There's ammo and a powerup on the platform. That switch on the platform just raises another platform nearby so you can reach an item floating in the air.

Hit the switch by the door to power the door up. Inside is a long hallway, which is blocked at the far end by a forcefield. You'll need to find a way to shut it down; for now this route is a dead-end. Try to avoid destroying the barrels when you fight the LSD. Here's why: before you leave, look by the door for a big crack up on the wall, open to the sky. Jump onto the barrels, then up into the crack, where there's an item and most importantly a Secret Level Access Keycard. (If you destroyed the barrels, you can just reach it by doing a running jump from the step nearby.) In each episode, every level prior to the secret level itself, other than the intro and boss levels, will have one Secret Level Access Keycard. Be sure you have it before exiting.

Lower rooms
Go back to the room with the platform, and follow the conveyor down to a lower room with a second conveyor and a glass construct in the center. There's a good deal of ammo and items in here, so explore carefully. Shoot the wall and crystal-egg pylon behind the conveyor you came in on for a secret area. When you're done, follow the second conveyor to a tall room with an arcing power conduit up on a column. Destroy the conduit to disable the forcefields. (There's a Weapon Enhancement Chip floating in the air behind the conduit.) Back in the conveyor in the tunnel, look for a misaligned texture on the wall. There's a secret area inside.

Exit and extras
Return to the long hallway, where you can now continue. Past the forcefield is a big room with computers and consoles. The exit is at the far end: that texture with the black and red animated V-shaped symbol denotes level exits throughout the game. Before you leave, find and hit the switch on the wall behind the column. This opens a secret teleporter behind the video display, which leads back to the concourse outside. Remember the overlook by the level entrance, where there was a forcefield? You can get inside there now. Go there, and ride the overhead Mazrium platforms to the far end of the concourse where they go to that passage up on the wall. There're items here. When you're done, return to the computer room and exit the level.

(It's also possible to jump to the platforms from the switch-activated platform by the entrance, but you have to time it just right. But this is only useful if you want the Li'l Buddy right away when you first start the level. You still need to hit the switch in the computer room to open up the passages in the walls that the platforms go through, in order to reach the items inside.)