Mass Effect's major villain was Saren Arterius, a rogue Spectre who had an army of Geth backing him up. He was the one who attacked the colony world of Eden Prime, prompting Commander Shepard to become the first human Spectre and confront him in a battle for the galaxy. And Saren almost won.
There is no doubt that, if Saren had gotten his way, the galaxy would have been doomed as the Reaper fleets poured in from the Citadel. The scary thing is that Saren's plan was smartly executed and wasn't entirely misguided. Saren put a lot of thought into it, and he got very little wrong. That's what makes him so relevant and dangerous.
Saren fell under the sway of Sovereign, becoming a high-functioning indoctrinated agent of the Reapers. He was no husk; he could still think for himself, but he was forced to put the Reapers' needs first. Saren himself explained to Shepard on Virmire that Sovereign needed to hold back on indoctrination, or else Saren would be a blubbering wreck. So, Saren hatched a plan to usher in the Reaper fleets, and he proved far more resourceful than any villain the galaxy has ever seen.
The Citadel was the key, since it served as a giant mass relay for Reaper use, but the Protheans had disabled the "open the Citadel" signal system. Saren needed a way to undo that plot. Touching the Prothean beacon on Eden Prime gave Saren some insights, and he sent his minion, Matriarch Benezia, to extract vital intel from the last Rachni queen to find the fabled Mu Relay.
Next, Saren obtained the Cipher, or Prothean knowledge, from the ancient Thorian creature on Feros to determine where he should go via the Mu Relay. Saren made his way to Ilos at once, and used the miniature mass relay there to warp himself into the Citadel and attempt to undo the Prothean sabotage.
Under ordinary circumstances, this would be a near-perfect plan, including some contingencies involving Geth and Krogan armies. Saren was breeding cloned Krogan on Virmire to protect himself from his enemies and aid his Reaper allies once they arrived. That, combined with Saren's secrecy, would protect his plan from all interference.
No army could handle Saren's Geth or Krogan, and no agent could track Saren's true intentions or beat him to the Mu Relay. Who else could possibly think to obtain ancient thought patterns from a plant or interrogate a hidden Rachni queen? Only the cunning genius of Commander Shepard gave the galaxy a fighting chance, and anyone else would have failed to apprehend Saren. His plan was too slick otherwise, and Saren was thinking ahead on yet another level.
Saren claimed that he was being useful to the Reapers, and that they would spare him and a few other "chosen ones" once they arrived. In reality, the Reapers saw Saren as a disposable minion, which is exactly how Saren viewed his own Geth and Krogan allies. Saren argued that since the Protheans fought back instead of surrendering to the Reapers' will, they were wiped out as punishment, which is partially true. Peace with the Reapers really is possible, but Saren was missing a key component: the Catalyst.
The Citadel hides many secrets, with its giant mass effect relay systems being just the start. This station also housed the Catalyst, the Leviathan AI that controlled the Reapers while seeking a solution to the "organics versus synthetics" problem. As Shepard later learned, synthesis can blend organics and synthetics into a harmonious whole, and Shepard has the option to pursue that route later.
Saren would have done that if he could, but his original plan would only let the Reapers into the galaxy, not fuse with them. Saren didn't even know about the Catalyst, so while his "unite with the Reapers" plan was correct in theory, it couldn't be done in practice -- especially since Saren was already indoctrinated. It was for the galaxy's benefit that Shepard finished off the visionary Saren.
Interestingly, Saren's philosophy would be repeated by the Illusive Man, who was also indoctrinated. He too sought unity with the Reapers to harness their power and unlock the future. The Catalyst (taking the form of a boy) confirmed that the Illusive Man had the right idea, but once again, indoctrination got in the way.
Saren's and the Illusive Man's dreams of the future would rest in Commander Shepard's hands, who could choose the synthesis route and bring an end to the organics versus synthetics dilemma once and for all. To his credit, Saren saw it coming and had most of the pieces in place to make it happen -- but only Commander Shepard could finish the job.
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