Swim down the tunnel, blasting fans that block your progress. Eventually you emerge in a chamber with three doors, kill the Skaarj in here and go through the only door thatll open. This leads to a platform that takes you to a balcony overlooking he first chamber. Follow the balcony into a control room, kill the Skaarj in here and press the computer console to open the main bay doors downstairs.
Return downstairs and go through the doors, press a button to summon a lift and ride it up to the Hangar. This contains a small hovering spacecraft and a shimmering force field.
Ride a lift up to a balcony and go through a door to reach a control room with three computer consoles. The left most console opens the secondary bay doors, the middle one drops the force field and the right one controls the main bay door you came in through. Press the left then return to the Hangar floor and through the new door. Downstairs press the button on the side of the glowing green generator, press a button on the wall and go through the door it opens. Follow a corridor outside and the proceed along a ridge until you reach the Nali church. Youll need the kill the Krall inside and then go through the wooden door, up a flight of stairs to a control room. Press the computer console and return to the churches main floor. Press the button on the other side of the churches main room to open a security door. Follow the stairs all the way down to a crypt. At the other end of the misty hallways is a high tech door, go through into the teleportation chamber. Press the computer console on the other side, a glowing white sphere appears on the lower level of the room, leap down into the sphere to teleport to the next level.