Sub Base Shock

Enter the shack south of where you started.

Enter the aquatic tank with the karkian.

Enter the keypad locked storage room by the guard room in the main module. The code is easy as 123. Actually, its easier than that. :-)

Enter the sub bay, where you find the mini-sub to reach the base.

Swim to the end of the flooded southern portion of the base. Its what the arrow labeled #3 points to in this pic from the walkthrough.

Advancement Bonus (400 pts.):

Enter the keypad locked passage that leads to the excavation area.

Enter the hall off the lift from the crew module. It leads to the last map where you get the schematics.

Get the schematics from the computer deep within the sub base.

Talk with Dr. Savage atop the command module. If you have a full inventory keep talking with him you may receive extra skill points and/or augmentation upgrade canisters depending on how patched your Deus Ex is.

Enter the short hallway leading to the launch command and silo entrances.

Kill or disable all three MiBs in the launch control room. Though I think this should be for aborting the launch its for disabling these guys you earn the points.

Reprogram the missile destination and reinitiate launch sequence.