The world didn't end. Desmond died, but released Juno in the process. Minerva warned Desmond that if she escaped she'd enslave mankind, which she will presumably begin doing in AC4.
Connor has an epilogue after the credits. You may have missed it. He burns all the portraits of his targets and removes the hatchet from the doorpost at the manor, signifying that his personal war is over.
There's a couple of cutscenes you can trigger in New York and the frontier once you take control of Connor again, too.
''Snake from Metal Gear 2 owns everybody. Because he used an owl. To make a guard think it was night time. In the middle of the day. That's just hardcore''