I'm still trying to figure out what the sun flares have to do with the Templars. What was the whole point of Desmond's story if there was not finale with the Templars? It's like they let someone who writes Ancient Aliens write Desmond's story.
the solar flares have nothing to do with the templars. if you really must know, the story of Desmond starts out as abstergo's plan to find the apple (with the power of dominance) to use in their Eye project, which would have launched a sattelite containing the apple to orbit, thereby allowing the templars to mind control people on a massive scale. during the search for the apple, it is then revealed to Desmond through Ezio that there is a solar flare approaching, that said solar flare is apparently a repeating phenomena, and that Desmond and his crew do not have much time to stop it. from there the whole paradigm of the goals for his animus training shifts, from learning to be an assassin to take down templars to reliving his ancestors memories to understand how to prevent the solar flare from ending the world.