Walk to a pair of computer consoles and read them, then save the game. Note the door ahead that’s labelled "Transformer Room". There are 3 transformer rooms in the immediate area all connected by shorts hallways. You need to sprint into all three rooms, dodging a pair of pursuing Skaarj and press a button in all three rooms.
When you’ve pressed all three buttons, an electrical barrier guarding the Science Research Lab is dropped. Run through the open lab door, and when you get to the other side, press a button on the wall to reactivate the barrier, kill the Skaarj that get through before you’ve reactivated the barrier.
Go upstairs to a balcony circling the lab and find the control panel. Press it to open the Research Lab doors and hop down to enter the lab. The doors will close and lock behind you.
A control panel on the lower floor of the lab will open the door, but it also releases the Amoeba in the glass tube, you need to dodge it and wait for the door to open, before you exit press the button that opens the Crew Berths door.
Get out of the research Lab and into the Crew Berths area as quickly as possibly, you may have lost the Amoeba, if not, drop off the bridge in the Crew Berths area to a platform and quickly find a lift leading up. The Amoeba should be left at the bottom.
Inside the Crew Berths area, investigate the bunkrooms and kill the Skaarj. Go through the door at the end of the long bridge, kill the Skaarj with Eightballs behind it and go into a small room, take a lift upstairs to a flooded Observation Lounge. Kill the Skaarj and read the message on the wall console, then dive into the pool.
Look for an underwater gate, ignoring the detonations that rock the ship. Eventually one will know open the gate, swim down and press a button, your translator will read "Bridge Security Forcefield Override: Status Deactivated."
Now exit the Crew Berths area and go to the bridge, then ride a lift to the command centre, press a button near either of the chairs that overlook the consoles and view-port, and the chair will slide away to reveal a hole in the floor, drop into it, walk into the octagonal teleporter downstairs to get to the next level.