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Assassins Creed: Brotherhood Walkthrough Sequence 3: part 3

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Immediately after the cutscene, start sprinting behind the Borgia captain. i recommend locking on him since you don't want to accidentally kill innocent civillians.

When you're close enough, press the attack button to kill him.

When you've killed him, jump in the water towards the island.

Swim towards the bridge shown in the picture.

Climb on the pole and jump to the ledge of the bridge.

Move to the right and climb up the bridge.

Then simply climb the tower and ignite it.

After doing so go to the mark on your map.

Once again, go talk to the architect to finish the mission.

For the final mission all you need to do is go talk with Machiavelli and the others.

When you're done, go talk to the architect one last time to end this sequence.