Assassin's Creed II/Sequence 11: Alter Egos

All things come to he who waits
A pursuit guard delivering something and you'll need to follow him. Like other following missions, keep him in sight, but don't get too close. Despite the fact that your objective is stated to be "Capture the cargo from the ship.", do not tackle him. He runs and climbs a lot, so this is a little more difficult than other following missions. Start out by jumping down to the roof of the building below you, then climbing down the other side, closest to the exit from the Arsenale. When he gets out into the street, he'll start running so follow him until he starts walking again as he enters a little alleyway with a group mercenaries in it. He's not all that aware of his surroundings while he's running, but don't get close to him when he's walking.
 * Memory start: Enter the white marker on the top of the west wall inside the Arsenale.
 * Reward: 7,000ƒ

Follow him through the alley, and he'll stop before entering the next plaza and look behind him, so stay around the corner until he starts moving again. When he's walked through the courtyard and down some little alleyways, keep following him when he starts running again. Right after he jumps across a canal via a pole in the water, he'll head through an enclosed courtyard with guards on the opposite end. He stops at the well in the middle and turns around, so instead of following him into the courtyard, take the ladder up on the right. This will lead to a couple jumps between the two buildings, and while he's checking behind himself, you can cross the courtyard above by going from platform to platform on the left side. Keep going through to the other side of the buildings and jump to the platform above the street in front of the four guards below. From here you can follow the courier unnoticed from above.

He'll walk down the little alleyway, and you can jump along the beams above. He'll hop over a short canal, passing by a guard on the ground before continuing on through the alleys. When you run out of wooden walkways shortly afterward, head back down to street level to continue following him. When he gets around the first corner, he'll start running down a bigger street. Eventually he'll cross a bridge then veer off down another narrow alleyway and cross another canal. Follow him across the water, but wait there, as he first goes around the corner to the left, but then double back and goes the other way. When you see him run back past you and head to the right, follow him again in a circle around the building, then across a street. When he starts free running up the crates with the white sheets, just keep down the street without climbing, as he shortly jumps back down.

Here he'll start walking again, right up to some guards waiting at the entrance to another enclosed courtyard. When you get up to them a cut scene will play, showing the courier packing up the cargo in a box to give to the Spaniard, and you'll have 1:30 minutes to take out the courier so you can switch places with him. Run down the street and hire the courtesans to distract the four guards blocking the way, then, when the guard inside has walked away, run in an go straight to the courier, who is in a little area out of the way to the left. Quickly take him out to get his uniform and finish the memory.

Play along
You can't leave the area until you pick up the box next to the exit. When you do, the commander will tell you to stay in formation, which just means follow the other soldiers as they go meet up with the Spaniard. Don't worry too much about any formation, just stay near the commander and walk to the objective in the southeast. You can desynchronize by getting too far away from either the commander or the box, and be aware that even though you're in a soldier's uniform, you can still alert the other guards by doing suspicious stuff like knocking the crates out of people's hands.
 * Memory start: Automatic
 * Reward: 7,000ƒ, Apple of Eden, Venetian Cape

When you get to the meeting spot, you'll have the opportunity for some quick time events, after which you'll have to fight the Spaniard. Bare-handed counters will at least block his attack, but hidden blade counters don't work at all. He's is likewise unaffected by either smoke bombs or the pistol. Both sword and knife counters work well, as do grabs, and those should be your main strategies if you want a melee fight. Like most combatants, he can't block your knives and they take off nice chunks of his health. When you've depleted his life bar enough, he'll stop for a short cut scene, after which four of his soldiers will come join the fight. Don't worry about the Spaniard, as even if you fully deplete his health, the fight doesn't end until you've taken out the other soldiers. They're all susceptible to all normal counters and all except the brute can be grabbed, so they should pose much of a problem.

After another cut scene, the fight turns into a huge brawl with more soldiers and some of the friends you've met along your adventure. The goal now is to take out the Spaniard, Rodrigo Borgia. Although you'll likely have other enemies on you at this point, concentrate on Borgia, as he's the main target. When you've beaten him, Borgia escapes and you'll watch another cut scene, after which just perform a leap of faith from the tower to end the memory.

Moving on
See the note at the beginning of Sequence 14 for the requirements to progress to the final DNA Sequence.