I think the templers know about the approaching apocalyptic event, but while the Assassins are trying to stop it, the templers are going to let it happen and then use the the pieces of eden rebuild the earth into their vision.
**Now I have yet to play AC2:BH but my friend did spoil the ending for me (not really I was at his house when he beat it) so if you haven't played it read no further.**
I think where the writers are taking the story is Desmond must find "his" "EVE" and that is the only way to re-enter the "garden", which will be the only safe place on Earth to survive the "event". Then after the "event" the story of life comes full cycle and Desmond and his "eve" will have to rebuild humanity since they are the only two left.
I know in AC2 it said people survived all around the globe last time, but I am thinking this time its going to be an "event" that wipes out everyone.