Yui is the mother of Shinji Ikari and the wife of Gendo Ikari. She was a brilliant bioengineer who worked on Project E at Gehirn. Additionally, she is the daughter of a prominent member of Seele.
Yui Ikari is one of the more powerful presences in the series. She is depicted as kind, optimistic, and motherly. Her faith in humanity and belief that it is worth preserving stand out compared to the more cynical characters in the cast.
Yui became romantically involved with a mysterious man named Gendo Rokubungi, several years older than herself. He was constantly the subject of shady rumors, including that he approached Yui for her talent and her connection to Seele. Nevertheless, in Yui's own words, he was "quite a sweet person. It's just that no one knows it."
In the rebuild film series, she is referred to as Ayanami Yui instead of Ikari Yui.
Yui took up work at the Artificial Evolution Laboratory in Hakone, Japan, which was really a front for Seele's secret research organization, Gehirn. Her skills in bioengineering were directed towards the "Adam Revival Project," also known as "Project E." In 2004, Yui volunteered herself as the test subject for the Contact Experiment with the incomplete Eva-01. She brought the 4-year-old Shinji to the site of the experiment to show him "the bright future." The experiment resulted in a "freak accident" where her soul was absorbed into Eva-01's core, and her body reverted to LCL. Gendo subsequently attempted a "Salvage Operation" to recreate Yui's body and fix her soul back into it, but this failed, resulting in the creation of the first Rei Ayanami.
Yui's soul remained inside Eva-01 throughout the series, with her son Shinji piloting it to defeat the Angels. Despite Nerv's extensive system of restraints, Yui's soul could take control of the Eva's body when Shinji was in extreme danger. This control manifested itself in berserk mode, a state of greatly increased power and savagery.
She first moved independently in Episode 01, protecting Shinji from falling lights, and again in Episode 02, taking control and defeating Sachiel after Eva-01 shut down due to severe damage. In Episode 16, she made contact with Shinji and took control immediately before the life support systems failed, breaking out and killing the twelfth Angel, Leliel. Finally, she manifested in Episode 19 against the fourteenth Angel, Zeruel. This time, she not only took control over the Evangelion and quickly defeated the Angel but also ingested its S² Engine.
When Third Impact arrived and Rei III rejected Gendo, control was given to Shinji and ultimately Yui. After Shinji's rejection of The Human Instrumentality Project, Yui took the Spear of Longinus and floated out towards space, becoming an eternal testament to humanity's existence as Evangelion Unit-01.
Yui reveals to Gendo that she believes anyone can find Heaven if they have the will to survive and attain happiness. This belief is passed on to Shinji, first in his return to the physical world in Episode 20 and later in his choice to remain alive rather than accept Instrumentality. Yui's beliefs may also be exemplified in her romantic relationship with Gendo, though questions arise about whether he truly loved her or used her to get closer to Seele. His actions suggest he was not merely using her; conversely, since she kept some of her agenda secret from Gendo, she may have been using him.
In episode 21, Yui describes Gendo as "...quite a sweet person. It's just that no one knows it."
Yui has her own agenda, different from Seele's and ultimately different from Gendo's as well. Much, but not all, of her agenda is presented in the series.
After presumably graduating, Yui married Gendo, and he took on her surname. He became involved with Seele, joining the Katsuragi Expedition to serve as an auditor. It is not revealed what Yui was doing during this time. After Gendo returned, they had a child together, Shinji, who would have been named Rei if a girl.
She died in 2004 as a result of her Contact Experiment with Eva-01, but her spirit lives on within the Eva as eternal proof of humanity's existence.
