User blog comment:Master Sima Yi/Assassinews 05-08-'14 – Assassin's Creed: Rogue announced/@comment-24760042-20141119173901/@comment-3046679-20141120223835

No, he joins the Templars to stop the Assassins from finding more of those particular Temples with the "Trees of Eden".

But you can understand the man, someone sends him to fiddle with an ancient tech nobody really understands. It goes wrong, levels an entire city and kills thousands of people, so that naturally gives you some mental scarring.

And when you confront the people who sent you, they shut you out and then attempt to kill you when you try to stop them from uncovering more of those Temples, since this was a second time this happened, and now they know it's not a coincidence.

So he feels if the Templars have the means to stop the Assassins from using any more Temples, he'd throw his lot with them. It's simple and understandable, once you take a step back and see it as a whole.