The Master will take away your ability to use radar and make it hard 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 out your sword and fight 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 to spot the real Al Mualim--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 and look for the Piece of Eden in his hand. Once you see him, throw a knife at him. Then, just counterattack/grab break him. Repeat 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.