Hacket's Reaper-Investigator unit gets wind of Leviathan, a myth, via one of their squads headed by Doc Bryson. Shepard heads there, Bryson does a little minireveal about Leviathan, Bryson's assistant suddenly goes nuclear and shoots the guy before blacking out - clear indoctrination. Shepard searches lab, finds lots of cool fun shit, finds a lead to an asteroid facility to find a Doc Frenchy (not the real name, of course).
Shepard goes to asteroid base, everyone is basically a zombie. Non-hostile, "Leave/You don't belong" type of zombie. Shepard breaks in, finds the Doc. Doc is indoctrinated, starts Reaper-speaking, chase ensues to find an artifact he had discovered. Chase ends at artifact, Doc suicides blowing up the artifact... except the real doc was dead the entire time at the artifact's base. Miners come out, reveal that they had been indoctrinated for 10 years and completely unaware of anything.
Shepard returns to Bryson's base, research, research, Bryson couldn't figure out how the artifact worked (He has one at his research base). They *do* flip a shield on to eliminate it's indoctrination though. Find link to his daughter, doing parallel research. Shepard rescues daughter, brings her back to dad's house. She surmises that the artifact is inert unless in use, then volunteers to be indoctrinated so they can trace the signal.
Shepard traces signal, goes to Waterworld. Shuttle gets blown out of the sky by Leviathan, but electronics not fried... just rendered inert? Exploration on the downed cruiser they luckily landed on finds that it was Alliance, survivors were slowly driven insane/subverted by artifacts until they cannibalized each other, then eventually died. In the distance are other spaceships of unrecognizable (read: Ancient) design. Reaper followed Shep to planet, sends waves of dudes who obviously die. They find the Triton, which is the underwater Atlas. Cortez realizes after fixing the shuttle that it still won't work, magically. Shep takes a trip 3000 meters under the sea.
Shep meets Leviathans, things are learned as detailed below. Shep convinces them that their cover is blown, and despite not wanting to assist Shepard or any 'lesser species' realize that they will die if all the Reapers converge on them. Shep is released, gets to surface, Reaper closes in... and Leviathans enslave it.