AC1 - The Templars are evil because that's just how it was back then. No huge conspiracy is revealed yet. By the end it's revealed the Templars are trying to find Pieces of Eden to control the population and push their "agenda", whatever that is. Truth or something. Hints at First Civ. AC2 - Get more Pieces of Eden because Templars are bad, mkay. More First Civ hints, more info about Absertgo. ACB + ACR - Oh crap, the world's gonna end! But wait, why are we looking for the Apple and the other Pieces of Eden? Oh well, they'll stop it all somehow. Clearly, the Assassins have been working towards a goal of helping the future assassins prevent the end. The Templars are aware of the end of the world, and want the Pieces of Eden...for some reason... [spoiler]AC3 - World ends. The entire cataclysm that Juno and Minerva have been trying to preempt has reached a point where it cannot be stopped. But...the entire time they've been manipulating events to reach a certain endgame...Juno even says that the Templars and Assassins wasted hundreds of years. Then why the hell did they bother setting things up for Desmond? Why didn't they just tell Altair to go get the key and the power supplies and sail to America and stop it all? It makes no sense. Regardless, Desmond is forced to pick the option that the Templars would have chosen.[/spoiler] So what exactly where the Templars doing? They clearly knew about the apocalypse, and were organized enough to stop it. Throughout the entire series, every Templar leader the assassins kill reveals that the assassins are ignorant idiots messing with a larger plan...but that plan is never revealed.