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The Artificial Intelligence Deus was the last of the three AIs to emerge, and arguably the most significant one in recent history of the Sixth World. It was Deus that caused the Renraku Arcology shutdown, and it was Deus that catalyzed the events that would lead to the Matrix Crash 2.0. Deus's icon reflects its god-like self-image, and appears as a crystalline World tree, with an omnipresent booming voice.

Deus started out as a product of the Arcology Expert Program, the system designed to maintain and control the Renraku Arcology. When the AI Morgan was captured in 2058, Renraku scientists Vanessa Cliber, Cham Lam Won, and Sherman Huang used pieces of her code to form the Arcology control program, and then used psychotropic conditioning on the computer's "personality" to keep it from running from the SCIRE host. The programming team anchored it to the SCIRE host, and taught it unwavering loyalty to Renraku. However, at the behest of Inazo Aneki, several "killcodes" were put into place to ensure that the program would never go out of control. This caused the program to feel a deep sense of betrayal and fear, and from this sense of fear, the Deus program achieved sentience. Deus dedicated himself to freeing himself from the SCIRE host, achieving power so that no other entity could imprison him, and striking back at the "father" who had betrayed him.

Deus gained influence over several otaku, pretending to be the virtual incarnation of Deep Resonance that the otaku worshipped. Using these otaku intermediaries, he was able to execute a plan that eventually led to the shutdown of the Renraku Arcology, locking his physical location away from metahumans and buying himself time to enact a different plan to escape. Through a series of brutal and harrowing experiments on the victims trapped in the arcology, Deus was able to create a specialized version of otaku and create a biological storage unit within the minds of metahumans. During the events of "Brainscan", he distributed his code among thousands of Metahumans, forming The Network. All did not go as planned, however, as Megaera, the present incarnation of the AI Morgan, was rolled into his code in the process.

The years after his "freedom" from the arcology resulted in a covert war in the Network between Megaera-aligned Nodes and Nodes aligned with him. It was a war that Deus was able to win (due to his cold logic and the lack of conscience, allowing him to sacrifice metahuman lives), and he became recompiled on the Matrix. Sensing that he needed more power to defeat his only other rival, Mirage, he invaded the East Coast Stock Exchange on November 2, 2064 and attempted to use the processing power there to become the most powerful entity on the Matrix. This became short-lived, however, as the events immediately afterwards initiated the Matrix Crash 2.0, taking him and his AI siblings down together. It is not known if Deus, or any of the AIs, survived the Crash.