The villain is extinction (literal contra-vida) via reapers.
Hmm. Depending on how you read the story, humanity always wins, just with different colors (destroy, control, syntesize), or there's a personal challenge that needs to be overcome.
Did you play a pirated copy? Galactic readiness/EMS is scripted to fall towards the end, locking you out of the real ending(s). There might be new cracks of ME3 that circumvent this.