The "villain" to me is the Catalyst; the Reapers themselves are pretty much slaves... no matter whether you pick red, green or blue, the Catalyst is destroyed, so the options then become:
1: the Red (renegade) option : kill the Catalyst, its slaves, the Geth and EDI - save the organics. I say this is the Renegade option because it gets the job done, no matter the cost.
2: the Blue (paragon) option : kill the Catalyst, gain control over the slaves and save everyone else. I only say this is the Paragon option because you're getting the job done at the cost of your own life - although it's a slightly grey area since you've become the Reaper-god.
3: the Green (wtf) option : kill the Catalyst and "Reaperise" everything else! Every plant, every fungus, every bird, mammal, reptile and amphibian becomes partly synthetic... the Geth and EDI presumably get Reaper upgrades, like when Legion upgrades the Geth, mixed with some organic components somehow. Everybody lives but there's nobody cheering in the Extended Cut ending. Everything about it is a bit wtf...
Synthesis doesn't kill the Catalyst. The only ending choices that have dialogue indicating that the Catalyst would be destroyed or replaced are Destroy and Control.
Destroy was intended to be the paragon ending and Control the renegade, though the Extended Cut introduced two different versions of Control. On a very low EMS playthrough Shepard will only have one choice at the end of the game. Destroy is the only choice available to a Shepard who chose to destroy the Collector base (a paragon decision) while the Control ending is the only option available to a Shepard who kept the Collector base (a renegade decision). Additionally the game uses Anderson (a paragon) as the avatar of Destroy and the Illusive Man (renegade) as the avatar for Control.





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