Storming the fortress right out is a good way to get dead, especially with the stealth snipers the game likes to throw at you. (One minute I'm fighting, the next I'm in a death pose, with no reason to be whatsoever. Thusly: Stealth snipers.)
The good way to do so, is to methodically reduce the number of guards there, so when the inevitable happens and you have to chase Germain to the real final battle, you can do so with peace of mind...
...unless you do something stupid and die, then the fraking guards respawn.
Germain + Sword of Eden...really? He was a twit before, and now you've given him a lightning sword? That zaps you until you die if he sees you, AND he uses Eagle Vision to spot you AND call down the lightning on your position?
But, you do eventually kill him...after Elise dies in an explosion during her attempted Revenge!Kill...
I'm gonna guess the Paris Assassins chose to look the other way when they gave Arno his Master Robes.
And the ending...heh, heh...Why, of course Abstergo, you can have his bones for your little project. You just have to find them first. In the catacombs. Under Paris. You know, the one filled with dozens of skeletons?
Mind the hallucinations.