Requiem
You'll be back at the Borgia strong hold to gain the final secrets of the Apple of Eden. It's more about stealth and climbing, but be sure to kill off guards that could easily blow your cover. Swing across the planks ahead and scale over the walls until entering the interior.
On the inside you'll need to climb up the planks and circle around the entire narrow hall way. Using Eagle Vision can be a great means for finding where to go next. Finally, move up the shaft above to reach the main floor. Exit to the roof, kill the guards and watch a scene as the Borgia clash at each other's throats.
An Apple a Day
Head to the roof of the castle and scale more walls, killing guards all along the way. Meet with Lucrezia to learn what happened. Proceed to the basement and chase after Cesare.
Move to the wall on the right and jump to the hanging platforms. Leap across the beams on the center of the room and then move up the shaft on the left.
You'll be back on the roofs and will have a bird's eye view of Cesare trying to escape. Keep on his tail and dive into the water below. Rush to the Vatican and dodge any Borgia pursuers. Hide in places or kill the guards that get to close. Even if you make it to the target you'll need to kill off any enemy before time expires.
The Apple of Eden
With the coast clear, move to the statue in the center of the court yard to discover the Apple of Eden. From now on you will not be able to change weapons and will have to charge the Apple to perform area of effect damage. Not only can this stun enemies, but it may cause them to attack one another. However, keep in mind that you will take damage while using the Apple. Stop and heal before making too many quick attacks.
Dozens of Borgia soldiers will swarm you, but the apple is enough to force them out of control and make them hack each other to bits. When all of the initial guards re dead, flee from Borgia territory (Marked yellow on your map) and return to your hideout.
Demilitarization
With the apple in hand, you now have the means to destroy the Borgia for good. Head to the town square and destroy the various captains around, all clearly marked on your map as main targets.
Like before, the apple drains your life, so be careful when using it too quickly. Otherwise, cleaning up the soldiers is no hard task.
Seeing Red
Your next task is to finish up the remaining guards around the Coliseum.
Take down the enemies outside and force them to kill each other from the Apple's power. Wait for the noble below and follow him to the rest of the Borgia.
In the main hall, call in your assassins and wreak havoc as you spam the Apple's power. Take out the main captains to send the rest of the troops fleeing, ending the Memory for good.
All Roads Lead to...
For the last part of the Sequence you'll be confronting Cesare directly. You'll have the support of Bart, La Volpe, Claudia, and Machiavelli. To make it even more chaotic, call in all six of your available assassins to keep the Borgia at bay
Keep using the Apple, each time waiting to recharge your life. Keep fighting until the timer runs out. Move to the city's gate to finally banish the Borgia and Cesare from Rome.