When fighting the Master he will take away your ability to use radar and make it difficult to see. This also allows him to hit you once and kill you. Lock on to him and use a throwing knife against him. This will take away his power to blind you and make him easier to kill.

The first part is simple. Take your sword out, as you will be fighting all your previous assassination targets. They are fairly easy to kill. Only one counter is required to kill each of them. For the second part, as soon as Al Mualim releases you, use your Eagle Vision. The real Al Mualim is the one in yellow. Focus your attacks on him. In the third part, Al Mualim takes away your synchronization bar and radar, allowing him to kill you in one hit. Take out your throwing knives. Look for the Piece of Eden in his hand. Once you see him, throw a knife at him. Thenm just counterattack/grab break him. Keep repeating this until he says, "Damn you Altair!" Finish him off with your hidden blade, or keep attacking him with your sword until he is dead.

When Al Mualim gets ready for the final part of the battle immediately after his third speech, lock on to him and equip your hidden blade. Move closer to him and when he is ready to attack, counter him to score an instant kill. He will fall to the ground and you can easily assassinate him without chasing him all over the courtyard. However, only do this if you have mastered the use of your counter attacks.