You start out in a small corridor leading to a lift. Press a button on the wall to call the lift and ride it up to a large dark room with crates and inhabited by Pupae and a Skaarj with a Stinger, use flares to help you see and kill everything in the immediate area. Find a ramp leading down and locate the glowing Generator Control computer panel downstairs, press it to light up the level and check the security panel on the other side of the room.
Return to the crate filled room, kill the Skaarj as they appear and take one of the ramps located on either side of the room to a door and a short corridor, then take a lift at the end of the corridor to a room with a Skaarj with a Stinger at work at a computer console. Kill it and activate the console and collect gear from the boxes at the side of the room. Take a corridor leading out of this room and walk through a teleporter, you’ll emerge in an arena with three Skaarj. Kill them and pass through the doorway to the Mothership basement.