(Major Spoilers, to those who want to be surprised!!)
It's going to be similar to the revival of the new star trek film series, in which a split timeline is created. As you all recall at the end 'Into the Wild Green Yonder' the crew fly into the giant wormhole, with leela telling Fry that she loves him before they go in. When they go in, two timelines will be created in some weird futurama fashion. In one timeline fry and leela will be together, they will most likely get married and live happily ever after. In the other timeline, the effects of the wormhole will have made everyone forget what happened before they flew in, which includes the fry and leela affair, and life will continue as normal in that timeline. The first episode will switch between the two timelines, showing what happens in each after the wormhole incident, it will be funny, romantic and sad, which answers the comments about it having it's "highs and lows". The series will likely continue with the timeline where fry and leela are not together. This way it keeps the fans happy about fry and leela ending up together (even if it is in another timeline), and also means they can continue on with the series back to what it originally was. So it really has echoes of the time paradox episode, and kind of 'Bender's big Score'. So there you have it, that's how it happens, personally I predicted that they will split fry and leela again, but at least this way they are together in another timeline, rather than them splitting up without anyone knowing why. Who knows, maybe we'll have episodes in the timeline where they are together.