Bioware is known for creating simply amazing, mind-boggling stories. What does Mass Effect have in store for us?
"Among those who study ancient ruins, a horrific legend is told: every 50,000 years a race of machines returns to harvest all organic civilizations. Few believe this ancient legend. Commander Shepard, however, knows it to be true. The fight to stop this extinction event has become his most important mission in the galaxy."
As you can see from this snippet, Bioware employs many talented and amazingly creative writers who surprise us all every time yet another storyline is created. In Mass Effect you discover information about an ancient race of mostly evil robots that was responsible for destroying galactic civilization roughly 50,000 years ago in a horrific cycle that resembles a "harvest" of organic life - and they're about to return! This storyline creates many questions like "evil robots?", "horrific cycle?", "harvest of organic life?", "return?" which, hopefully, will be answered in the third game.
It makes sense that Commander Shepard is the only person who's seen this evidence - and being the only one important and special enough to do something about it - he begins scouring the galaxy to destroy the agents of the machines and prevent the cycle from happening again. The president counts on Commander Shepard as the only man he can trust to find the robots and to stop the destruction of everything we hold dear.