Finally beat it and I avoided all of the spoilers. Hooray for me!
So this is what happens: You end up hanging out with God. God as he appears in the Bible seems somewhat child like, if you think about it. He's easily angered, jealous, loving, vengeful, etc. Anyway, you destroy the Mass Relays which basically destroy all of the universes and kills everyone. Even all of the races that chose to help you end up dead.
So, Joker and your crew try to outrun the battle since the Crucible isn't working and there is basically no point in continuing the fight (Cortez didn't die so he picks up some of your squad). They flee the reapers when the Mass Relays explode. They are flung somewhere way off in the universe.
The Cycle begins again with the universe starting over as an infant. Mankind has survived because the Normandy is somewhat of a "Noah's Ark". The people on board have started life on a new world (Very Eden like, too) with enough men and women to populate. Generations later, Sheperd is a figure of legend passed down from the crew that loved him/her so much.
Just like the Prothean character, Javik, whom Liara thought would be god-like, "The Sheperd" is just a guy with details obscured by history.
Best game series this gen.
