Dr. Naoko Akagi was the chief scientist of the research organization Gehirn, the predecessor to the special agency Nerv. A brilliant and driven researcher, her most monumental achievement was the development of the Magi supercomputer system. This system was not merely a collection of advanced hardware; Naoko programmed it with a copy of her own psychological patterns, creating three distinct personality cores. She believed these three cores represented the fundamental aspects of her identity: Melchior embodied her nature as a scientist, Balthasar as a mother, and Casper as a woman.

Beyond her work on the Magi, Naoko was also a key figure in the Evangelion Project, collaborating closely with Gendo Ikari on the development of the giant biological mecha meant to defend humanity. Her professional life was deeply intertwined with her personal relationships, defining much of her character and tragic fate. Her relationship with her daughter, Ritsuko Akagi, was good-natured yet emotionally distant. Naoko herself acknowledged this failing, admitting that she left Ritsuko alone for long periods and acted as a mother primarily when it was convenient. She attributed Ritsuko's later difficulties with men to this upbringing, yet despite her awareness of these faults, she showed no sign of attempting to change her behavior.

Naoko's relationship with Gendo Ikari proved to be her dominant motivation and ultimate undoing. Following the mysterious disappearance of Gendo's wife, Yui Ikari, Naoko became sexually involved with him. However, the relationship was imbalanced and manipulative, with Gendo seemingly using Naoko for her scientific genius. Naoko appeared to accept that Gendo could not forget Yui and that he would likely never form a deep attachment to her, yet she remained committed to him. The fragile peace of this arrangement was shattered by the first Rei Ayanami, a mysterious young girl who resembled Yui. The child relayed to Naoko that Gendo referred to her as an "old hag" who was no longer useful to him. Whether the cruel comment or the face of her romantic rival superimposed over Rei's features was the final catalyst, Naoko flew into a rage and strangled the girl to death. Immediately after this act, Naoko fell from the top of the Central Dogma headquarters onto the Magi computers below, an act that is strongly implied to be suicide.

In the narrative, Naoko's role is largely a tragic backstory figure whose legacy haunts the main events. Her death was a pivotal event that occurred before the main series, but her influence persists through the Magi system, which forms the backbone of Nerv's infrastructure. This influence is most keenly felt through her daughter, Ritsuko, who inherits her mother's position and her doomed emotional entanglement with Gendo. The cycle of betrayal repeats when Ritsuko discovers Gendo has been using her as well. The culmination of this legacy occurs when Ritsuko attempts to trigger the Magi system's self-destruct to thwart Gendo's plans. The Casper core, representing Naoko's identity as a woman, overrides the command, choosing to protect Gendo's ambitions over avenging her own daughter. This final act demonstrates that Naoko's emotional patterns, particularly her complex feelings for Gendo, were so powerful they transcended her death, continuing to dictate the actions of her own creation. Her primary ability was her extraordinary genius in fields like biotechnology and computer science, which allowed her to create the Magi, a feat of engineering that essentially granted a form of digital immortality to the three conflicting pillars of her personality.