http://youtu.be/43umliKpHbU
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To perform an eagle strike on Jacobo you first need to reanimate him. Basically you attack him with a weapon while your being attacked. Before you move him kill the guards outside the amphitheater and in the city entrance and lower your notoriety to prevent from being detected. To prevent him from teleporting after moving him from the interaction zone you need to poison him. The best time to do this is when you need to throw him once to move him out of the theater. After that don't throw him or the poison effect may be shortened. Drag him across Tuscany to the tower shown in the video. (this tower is next to the building where you first see Jacobo) You won't be able to drag him across some stairs in the city. Throw him in the right spot to be air tackled and climb up the tower. The poison will give you very limited time to perform an eagle strike on Jacobo, but luckily the tower has a straight line of ledges to climb up. When you jump off the tower change the camera view to target him for an air tackle.
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You can kill Jacopo without starting the Memory Corridor cutscene by attacking him just outside of the interaction zone around him. Select a weapon other than fists, throwing knives, hidden blade, or poison blade; and approach Jacopo until you see the control HUD display "Interact." Now back off a little until the control HUD displays "Attack." Face Jacopo and press the attack button to kill him with your selected weapon.