Objectives: Find an Envirosuit and Sonic Emitter
Well, something ominous certainly occurred down here, as the bodies lying about should attest. Search the footlockers here, then head south to run into a very distressed mercenary. After ignoring him completely, go east to find the main area of the base, populated by insane Selkath and roaming droids. There's a fairly simple map layout, and few areas of real interest, so just explore until you find both a sonic emitter (there are two of these in footlockers on this level) and an envirosuit (found in the envirosuit storage section of the station, as marked on your map). When you have both of these, head to the airlock in the middle of the Station's southern side. You'll have to leave your teammates behind for the duration of this mission, so kiss them farewell and step out the airlock.
Sea Floor
Objectives: Get to the Kolto Control facility
This area is the standard model for why walk-throughs exist: to avoid tedium. Your envirosuit is very pretty, but it's also quite slow, and there's nothing you can do to speed yourself up. Luckily, there's a fairly direct path that you can follow.
First off, from your entrance point, take a right to speak to another survivor of the disaster; he'll say that he's heading out to the sea floor. There's only one path to the south (if you head west, you'll be rewarded with two average frag mines in a footlocker, so skip it), so follow your mercenary companion that way.
Exeunt companion stage left, and welcome benthic explorer, to the dreaded vastness of the ocean floor. Head west to run into the sharks, which BioWare, apparently feeling miffed at Sid Meier, have named "firaxa". You can take them out with one shot of your sonic emitter, but, to keep things even, they can kill you in one shot as well. Needless to say, keep your finger on the trigger. If you find yourself getting stuck in the emission animation after taking out a firaxa, don't fret; just sit there for a second and you'll eventually regain control of your character.
Anyway, head west, being sure to loop back into the smashed window to pick up a nerve amplifier belt, and eventually you'll wind up staring at the kolto control facility. Take the southern entrance inside.
Kolto Control
Objectives: Discover the origin of the disaster
You're on your own here, so keep those Force powers at the ready. Once you reach the central room, you'll come across Kono Nolan and Sami, two of the Republic scientists. They'll try to kill you, as all good folks should. You can talk them out of their mistake by banging on the force field repeatedly, or just run over to the computer and hack it to shut down the depressurization fans.
When you calm the pair down, you'll finally learn a bit about what the hell has been happening down here. In sum: there is a monster shark. You must kill it. You have two options: Kono suggests that you attempt to poison the creature by placing a kind of blistering agent in the kolto harvesting machine, and then venting it into the water, which should destroy the beast, but may also have serious side effects on the surrounding environment; Sami thinks you should destroy the drilling equipment that seems to have stirred the monster from its chthonic lair. Either way, you'll need to suit up once again and head back out onto the ocean floor through the airlock behind Kono and Sami.