I didn't get a captcha this time, so I'll use one that I remember fondly: The Isocrons.
The Isocrons are a race of peaceful alien bio-robots who live alongside humans in the future. They come in many shapes and sizes, some like animals, some like humans. They kind of belong to a hive-mind, but not really. They are free to make their own choices, but they can contact their matriarch telepathically at any time. However, a virus infected her is turning the Isocrons into, essentially, zombies of varying intelligence levels. In this future, guns are highly regulated by the government, so guns are extremely rare to come across being used by anyone but the military. They are also really expensive on the black market, and cheap ones are prone to miss-fire and/or break easily, so a lot of the combat until late in the game is melee-based, using knives and other assorted blades to defend yourself. By the end of the game, all of the Isocrons are infected, and the only way to kill the virus permanently is to wipe out their matriarch in a long, climactic battle full of lasers and space-dreadnoughts. Killing the Isocron matriarch also kills all of the remaining Isocrons. So you have the choice: Kill her and wipe out an entire species, or isolate the Isocrons for what could be forever and try to search for a way to cure the virus.
You play as an ordinary person on the human colony on Saturn's moon of Titan. Titan's Isocrons were the first to succumb to the virus, and you are one of the sole survivors of this carnage, almost completely due to dumb luck. Being an ordinary, person, you aren't all that strong or all that fast, nor can you fight very well. Considering the only weapons you can get at first are knives, you're pretty much helpless. Gameplay-wise, it starts out as a Action-Horror game, with a much greater emphasis on the action. About two-thirds of the way through, you are rescued from Titan by the human military and brought to a training camp on Mars, due to you being the only person they could find with much experience against the Isocrons. You spend a couple yeas there training. By the time you're ready, more than half of the human colonies in the galaxy have fallen to the Isocrons, including Earth. You receive a standard-issue rifle and powered armour, and the game becomes more like a shooter.
Wow, I put a lot of thought into this...