Mass Effect 3 - Shepard's Indoctrination
Don’t watch if you don’t want spoilers!
By itself, the Mass Effect 3 ending makes very, very little sense, but the Indoctrination theory is about the only reasonable explanation I’ve came across that ties everything together in a decent fashion.
The other, unreasonable, explanation is that the ME3 writers were idiots and pulled the ending out of their asses at the last minute, throwing away any trilogy arc material that may have existed.