I was confused about this,
"To help the Templars..."
You're actually fighting the Templars, helping the Assassins. :P
I think the trailer at the site might explain it. The Templars got their hands on a bunch of Animus machines? Maybe?
I just use what the press release gives me: "For the first time, Assassin’s Creed Brotherhood offers a never-before-seen multiplayer layer. Players can help the Templars by using Abstergo to train in the art of Assassination to eliminate the Assassins once and for all."
Maybe it's different for the multiplayer? Don't know. All I know is that I get upset during the first game because it won't let me just gallop around without setting off alerts and that's stupid.