Rodney destroys the universe

In this story, Rodney indeed destroys the universe at Doranda and He, John and Weir barely make it back to Atlantis with their skins intact, however Atlantis is empty as they have also gone back in time... science; it's complicated.  Rodney has grave difficulty grappling with what he has done and John and Elizabeth aren't all that happy either.  That's it, that's all I remember, except they do start going through the gate (or they'll starve) and make alliances, etc.  Don't remember who this all wrapped up, except it's one of those hellacious melancholy endings (which I love).  Anyone?