Prior to your sojourn to Virmire, the player is only vaguely aware of what it is that he's fighting against. A renegade spectre named Saren is going to bring back an ancient machine race known as the 'reapers', but to this point, all you've seen of these creatures consists of creepy, vague visions.
Then you walk up to a console in Saren's base, and suddenly you're talking face to face with one.
|Oh, hi there.|
"You exist because you allow it and you will end because we demand it."
With just a couple of minutes of dialog, Saren goes from being the diabolical mastermind to an unwitting pawn in a game beyond his understanding - and you go from a standard "hunt the bad guy" scenario to a near-impossible race against the clock to ensure that a galaxy-wide doomsday is postponed.
That's right. Not averted. Not cancelled. Merely postponed. As Sovereign makes abundantly clear in his chat with Shepherd, there are thousands upon thousands like him, just waiting to harvest the creatures of the galaxy. If Sovereign falls a bit into the trope of the villain tipping his hand to the hero, he has better reason than most. This cycle has happened countless times, to civilizations much more powerful than those that currently occupy the worlds that the Reapers cultivated them in.
...and then the trip really takes a turn for the worse.