Let me start by saying this is in no way a complaint towards the New 52 just honestly what fan wouldn't dream about what they would do if they had the chance?
I would begin with the Greek Gods returning to earth and awakening the Amazons from a suspended animation that they had put them in. Some time after that they would use the Amazons to help wage war on the Earth as the Greek Gods try to set up their rule of the Earth once again. This would bring out Earths greatest heroes and Superman, Batman, Green Lantern, Zatanna, Flash, Dr. Light, Martian Manhunter, Firestorm (Jason Rusch), Atom (Ryan Choi), Zauriel, and Aquaman. In the end Wonder Woman discovers that the Greek Gods are really aliens and feels betrayed and joins the fight with the rest of earths heroes to defeat the Gods. Then within a year or so of this event I would have the arrival of the New Gods who had killed the Greek Gods and taken their position in the universe.