Retaking of Masyaf

After killing Robert De Sable, Altair rides for Masyaf to speak with his master, Al Mualim. As he enters through the city gates, Masyaf seems different, no longer buzzing and social, now a deadly silent ghost town. Upon entering Masyaf, a man greets Altair, and upon asking where everyone is, the man replies "Al Mualim has shown us all the light! Long live the light!"

Altair decides that he must see Al Mualim and heads towards the Assassin's Fortress.

Altair vs. The Brotherhood

On the way to the Fortress, Altair sees some of the Assassins blocking his path. Upon seeing Altair, they draw their swords. Altair attempts to fight them off but there are too many, but just in the nick of time, Malik and some of the other Assassins who aren't being controlled by Al Mualim's Piece of Eden fight them off and save Altair.

Altair runs up to the top where Mailk and the others wait for him. Altair tells them what he has learned and suggests they try to find a way in through the back while he assaults the fortress from the front.

Altair and Malik go their separate ways and Altair goes to the Assassin's Fortress. Standing in front of the Fortress are a large group of Al Mualim's mind slaves. Careful not to hurt any of them, Altair makes his way through the crowd and into the Fortress.

The Battle With Al Mualim

Altair sees the door to the Assassin's Garden is open and decides to see if Al Mualim is outside. As he steps outside, at which point the door shuts behind him and he is captivated by the spell of Al Mualim's Piece of Eden. After a taunt, Al Mualim reveals himself and explains to Altair why he never used the Piece of Eden to enslave him. "Who you are and what you do are too closely related, to enslave you would be a waste of your skill." Al Mualim explains what the Piece of Eden does and how it works, and decides to test Altair's skill against his Master's.

Using the Piece of Eden, Al Mualim reanimates the corpes of those Altair kills, but Altair picks them off one by one. Al Mualim then decides to change his tactic, and once again using the Piece of Eden, he clones himself, but Altair uses his Eagle Vision to see past the wizardry and see the real Al Mualim, striking him with his blade, the clones disappear. In a last attempt, Al Muallim disappears and re-appears somewhere else in the garden, but also uses the Piece of Eden to make Altair weak, but after striking Al Mualim, he regains his strength. Al Mualim finally gives up with the tricks, realising that Altair can overcome them.

Al Mualim decides to have a battle one on one with Altair, but is significantly weak after using the Piece of Eden, and so Altair kills him. In his dying words, Al Mualim explains why he wanted to the Holy Land and why he used the Piece of Eden. Al Mualim asks Altair what he's going to do with the Piece of Eden, to which he says "I shall destroy it in the hope that it shall never be used again." But as he goes to collect the Piece of Eden to destroy it, he feels compelled not to, and as he dies, Al Mualim ridicules Altair for not destroying it like he said he would.

After that, Malik and his gang turn up in time to see the location of the other Pieces of Eden around the world.