The Nexus was a disruption in time from where probabilities were calculated, to which the First Civilization had access. It was used by the First Civilization to predict the "proper path" for individuals or to speak with individuals from the future. The Nexus could be entered by activating a Crystal Ball, or by achieving a Synch Nexus with one's ancestors inside the Animus.
The Nexus was entered by the Kanien'kehá:ka named Ratonhnhaké:ton, by activating his tribe's Crystal Ball in 1769. He was greeted by Juno, who informed him that through maintaining his current path, it would lead to the destruction of his village. She instead directed him to become a member of the Assassin Order, knowing that this path would lead to him obtaining the key to unlock the door inside the Grand Temple. Ratonhnhaké:ton later entered the Nexus again in 1783 after he obtained the key, and Juno directed him to hide it where nobody would look for it, knowing that his descendant Desmond Miles would eventually find it.
In 2012, after Desmond Miles had fallen into a coma and his consciousness fell into the Black Room of the Animus, Desmond was told by Clay Kaczmarek that in order to regain his consciousness and prevent the memories of his ancestors from overlapping with his, he needed to achieve a Synch Nexus; relive all unfinished memories of his ancestor, Ezio Auditore da Firenze, inside his DNA. Desmond then proceeded to relive the remaining memories of Ezio in the Animus, and was subsequently transported to the Nexus, where he was greeted by Jupiter. Jupiter then explained and showed him the aftermath of the First Disaster, and guided him to go to the Grand Temple, after which Desmond regained consciousness.
- "Nexus" was the original working title for Watch Dogs, another Ubisoft title.