Mass Effect 3 is Really About the Hero Getting Possessed by AliensEditThe Mass Effect games tell the story of intergalactic hero Shepard as he or she (the character's gender and appearance are totally up to you) does battle with the Reapers, an ancient race of super-huge robo aliens known for wiping out entire civilizations, because when you're a planetoid cyborg, what the hell else are you going to do? Their two methods of civilization murder are good old-fashioned destruction and Borg-like indoctrination wherein they assume control of living beings and bend them to their will (see Animal Crossing, above).
At the end of Mass Effect 3, you're given three options to supposedly end the Reaper threat: control the Reapers (Shepard dies), synthesis (which effectively turns everyone into Reapers), or destroy the Reapers (Shepard dies, probably). All in all, it's a pretty thankless and confusing way to end an epic trilogy (this is a phenomenon called "The Dark Knight Rises Effect").
Shepard was slowly being indoctrinated by the Reapers all along, across all three games, and the ending of Mass Effect 3 represents their final attempt to assimilate Shepard. There is a fucking two-hour documentary assembled by fans that laboriously goes over every possible clue in the series, but we're only going to talk about the ending.Toward the end of Mass Effect 3, Shepard gets blasted with a powerful dose of Reaper energy, like a hose of evil psychic techno-alien anger juice. The series constantly emphasizes that people get indoctrinated after prolonged exposure to the Reapers (and Shepherd has been around them for three games at this point), so fans suggest that this herculean laser zap was the final straw, and that everything afterward is a result of the Reapers invading Shepard's mind. Check it out: After the blast, the world takes on the hazy fuzziness of a dream. Bodies mysteriously vanish from the battlefield and people appear out of thin air as if the rules of the universe no longer apply. Sounds a lot like a guy struggling with an alien-induced hallucination, right?
When you make the final choice to wield, join, or destroy the Reapers, all three options are color-coded, just like every other choice you've made in the entire series -- blue represents the good or just choice, green is neutral, and red is evil. Now look at this picture of the final choice in action:
You would assume that the obviously blue-hued selection would be to eliminate the Reapers and save the Earth (good), whereas the red-stained option would be to take control of them to rule the galaxy (evil), right? You'd be totally justified in thinking that, and you'd also be committing a huge space error, because that assumption is utterly incorrect. The blue choice is to control the Reapers, and the red choice is to destroy them (the middle choice is to join the Reapers, but if you make that selection you should just eject the game disc and snap it in half because you're playing it wrong).
So why would the blue choice suddenly be evil, when it's been good for the entire series? Because the Reapers are inside Shepard's mind, trying to influence your decision. We've already pointed out that it seems like Shepard is hallucinating during the entire final sequence -- the Reapers are just making Shepard see the evil choice as being the noble one in an effort to trick you into joining them and completing Shepard's indoctrination, and also to purchase all of the upcoming DLC packs.