You will start in a hallway with a window to your left. Note: there are roving shuttles that fly past these windows; they can hit you with rockets through the window. Turn around and enter the teleporter behind you.
You will land in a shuttle. Go forward to get the RPG, and use the security monitor to see a help message. Get the steroids under under the overhang, and go back into the teleporter.
Follow the hallway and turn left at the end to find a security monitor. Stepping up to the monitor opens a door high on the wall behind you; jump to it for RPG ammo. (secret) Go to the right and around the corner to find a wall covered in computers. Get the shotgun. Press open on the second computer panel (it will be broken when you first enter) to open a door to an atomic health. (secret) Flip the switch to the left of the computers to turn off the forcefield you just passed, and head through the doorway.
In this hallway is a drinking fountain you can use to restore your health. Go through the door to another hallway. You will end up in a room with big windows and a forcefield tube in the center. Walk ahead and enter the door on the right. Get the scuba gear, blue keycard, and portable medkit. Press open on the white section of wall. It will open to water; dive in to find a chaingun. (There is a shaft underwater that leads nowhere; it actually comes up behind the red keycard in the underwater area of the forcefield tube, but this never opens to allow access between the two areas.) Exit the water and go into the vent to your left. It opens up after a short distance; turn left, jump to the ledge, turn left again, and jump again to a low room with pipebombs. (secret) Drop down into the hallway you came through and go back to the main room.
Now, go to the left around the wall to find an elevator. Take it to the upper room. Use the security monitor if you wish, and open the right computer monitor to find a holoduke. Use the blue keycard; it will open the elevator at the far end of the room. Take that elevator.
In the next room, jump on the green box and up to the ledge to get the jetpack. Shoot the yellow C-9 tanks to blow the elevator shaft open. Go to the elevator shaft, and flip the switch inside. Turn around and go up the ramp. In the top room are combination switches (activated by the switch you just threw)- it starts as off/on/off/off; switch it to off/off/on/off. The forcefields tubes are now open. Exit to the main room. Jetpack up to the top-left of the wall toward the combo-lock room to get an atomic health. Turn the jetpack off and walk forward; you will hear a door open. Quickly, drop through the hole where the forcefield was. You will pass the previous floor and land in water.
Get out of the water, and you will be in the first room. Go to the area between the elevator and blue-keycard room for ammo (PC) or atomic healths (N64). (secret) It is timed; if you don't make it, go back to the atomic health spot in the previous room. Get back in the water and dive.
Get the red keycard, then turn around and hit the button to open a panel with atomic healths and a jetpack. Jetpack up, past the two levels you've seen, to a small hallway connecting the blasted elevator shaft to a lit-up room. Go to the room to find a monitor and devastator. (secret) Go back to the center shaft and use the jetpack to go up once more, to a space dome with a medkit and night vision goggles. Drop back to the floor with the combo switch.
Go back to the room with the combo switch and go through the door on the back wall. There is a light spot on the floor; press open while standing on it to descend to a lower level as an elevator. (secret) Go around behind the elevator to get the shrinker, then follow the duct above the floor, to the left of the elevator opening. It leads to an elevator that immediately takes off on its own; turn right and spring as soon as it hits the top to find a passage back out to the combo-switch room.
Go back through the door, over the elevator, and use the red key. Go through the sets of doors to find the level-end button behind a glass pane. Break the glass, push the button, and you're done.