During Assassin's Creed: Project Legacy, an Abstergo Industries recruit is put into an Animus machine, showing a memory of Mario Auditore preparing Monteriggioni's defenses for an attack from the Fiorentini. After harvesting lumber, recruiting new people for various jobs, harvesting from the local gardens and working out a mine, Mario began to train the citizens for combat and brining in his fellow assassins for the coming fight. The battle was fierce and deadly, and during the fight someone slashed Mario in the face, ruining one of his eyes, but the Monteriggioni citizens won the battle, and learned the Fiorentini weren't there for the city- but an artifact beneath it. Mario leads an expedition under the city, where they encounter fierce traps and some of them die, but they recover the box containing it- which he hides in the villa until his brother Giovanni can come and give it to the Brotherhood. Abstergo then cuts the memory off.
After the death of Giovanni Auditore and two of his sons, he took Ezio in and began to train him to fight, eventually revealing the secret history of their family- they were members of the ancient Assassin Order, pledged to fight the Templars, and it was they who were behind his father's murder. After completing his training Ezio planned to leave, angering Mario who was hoping he and his nephew could ride together to battle the Templar at Tuscany. At the last minute, Ezio changed his mind, and returned to help him, breaking into the city to open the gates from the inside out, allowing Mario and Mercenaries to attack. He also gave Ezio the chance to take down Vieri de'Pazzi. With this, Ezio finally accepts his role as an Assassin, and his Uncle continued to support him in his quest for many years.
After allowing Rodrigo Borgia to live after retrieving the Apple of Eden, Mario arrived to help Ezio sneak out of Roma. Despite his act of mercy, the Pope's son Cesare Borgia was able to follow them back to Monteriggioni, where his army laid siege to the city. While the defenses were strong, Cesare's forces were overwhelming, and they managed to get inside the city. While Ezio rushed to the gates, he saw Cesare had captured the Apple from the Grand Master of the Assassin Order, and shot him in the head, killing him.