Despite having grown apart from his friend after discovering he was homosexual, Javier agreed to help Owen with proving the innocence of the latter's father, who had died after being sent to prison. Owen wanted to use a clandestine Animus owned by the mysterious Monroe to relive the memories of his father's supposed bank robbery. Despite the fact that Monroe could not help Owen due to the limitations of the Animus, Javier's curiosity led them to use the Animus anyway. They subsequently experienced the genetic memories of their respective ancestors, who met during the Spanish conquest of the Aztec Empire.
During the session, Javier felt the power of one of the Pieces of Eden firsthand when Hernán Cortés used it on his ancestor Chimalpopoca. The discovery of clues potentially leading to the Trident of Eden also attracted the attention of both the Assassin Brotherhood and the Templar Order.
- During his Animus session, Javier was confused by the feelings of his heterosexual ancestors, notably the physical attraction Chimalpopoca felt for Cortés' lover, the beautiful Marina.