I got the Collector's edition so I don't know if this is something that is only on CE's. But currently I am in a Templar Lair with Mission called Liquid Gold and now the objective is to kill a Templar but I do not see any way to get up to kill him. I climbed up all the way till he sends his guards and mine workers at me but no way to kill him.
If you're on the lower level, facing his perch, look to the left. You'll see one of those swinging pots that you can use to go around corners. It'll take you to a place where you can go up to the second level to activate a lever. Do that, then you should get a cutscene showing a second lever on the opposite side. Go activate that, then return to activate the first lever again.
His platform will collapse and he'll flee.
Now playing : MAG, and promising to shotgun enemies and perform medic duties to the best of my abilities, to boot!