After their visit to Naples and their conversation with Camilla, Ezio Auditore da Firenze, Niccolò Machiavelli and Leonardo da Vinci immediately boarded a ship to Valencia, although it took them several hours of preparation before they were ready to depart. The Assassins' journey was difficult, as the sea was rough and they met many squalls that took the sails aback.
After a journey of five days, they had given up hope of reaching Valencia before Micheletto. They arrived in Valencia's harbor, where they immediately saw the ship Micheletto had used. They went to its owner to ask for directions, and he directed them to the Lone Wolf Inn.
Ezio, Leonardo and Machiavelli made their way to the Lone Wolf Inn with the intention of spending the night at the same place as their target. Once they arrived, they found the inn to be very dark, and the door to be open. Despite this, they entered the building, only to find themselves ambushed by a group of ten men that had been hiding in the shadows.
From this, a short and chaotic fight ensued, during which Ezio had a brief confrontation with Micheletto himself. When most of the ambushers were killed, Micheletto and his remaining followers fled the inn. Ezio attempted to give chase and managed to corner one of Micheletto's followers, who told them Micheletto had set off to the Castillo de la Mota, revealing it as Cesare's prison.
Escape from prison
The Assassins spent the night in the Lone Wolf Inn and rode off for the prison the following morning, occasionally asking directions. However, Micheletto had a good start on them and had planned Cesare's escape carefully. He and his followers managed to get Cesare out of his prison with the help of a bribed guard and their ropes, disguising Cesare as a guard as well.
When the Assassins finally arrived at the Castillo, they received the news that Cesare had escaped. Ezio remembered a vision the Apple of Eden gave him when he was still in Rome, and realized Cesare was headed for the harbor of Valencia. He wished to return immediately, but Leonardo fell ill, so they had to wait. Nevertheless, they returned to Valencia within the month.
Attack on the harbor
Once they returned to Valencia, the city was in uproar. Cesare had already gathered an army of a thousand men just outside of the city, and a fleet of fifteen warships, protected by half a dozen smaller ships. Machiavelli proposed to wait for the help of King Ferdinand II, but Ezio remarked it would take them far too long to even arrive at Valencia. However, Leonardo had a plan to stop Cesare, revealing to them a new invention: bombs. They gathered the necessary ingredients for the bombs, and two days later, Leonardo had finished them. He then traveled back to Italy, leaving Ezio and Machiavelli behind.
Ezio and Machiavelli split up, with Ezio heading for the ships and Machiavelli for the camp. The bombs proved very effective and they managed to destroy Cesare's forces without much trouble. After that, they decided to head for the Lone Wolf Inn again, as it was presumably what remained as Cesare's base of operations.
Death of Micheletto
On their arrival, the Assassins climbed the roof of the inn and looked through the windows to find the right room. Once they had located it, Ezio and Niccolò spotted Cesare and Micheletto; while spying on the pair, Cesare revealed his plans to travel to Viana since his army had been crushed by the Assassins, telling Micheletto that his brother-in-law, John III of Navarre, would help him. Micheletto then remarked that he was Cesare's right hand, and that he would help Cesare, but Cesare simply noted that Micheletto had failed him. Outraged, Micheletto charged at Cesare but was shot through the head.
Cesare then prepared to leave the inn, but Machiavelli kicked loose a tile, drawing his attention. With great speed, he took out a second pistol and shot Machiavelli through the shoulder. Ezio considered following Cesare but decided he had to bring his friend to a doctor first. Once there, they bid each other farewell and Ezio began his journey to Viana.
Cesare Borgia escaped from his prison, but his entire army was crushed before he could start his conquest of Italy. Micheletto Corella was killed by his former master, and Cesare set out for Viana, in the kingdom of Navarre. Following this, Ezio Auditore decided to follow Cesare on his own, as Machiavelli had to recover from his wound for at least two weeks.