The events of this story took place after Chapter 90.
Late at night, Ritsuko Akagi sat in her office. After taking a sip of coffee, she continued analyzing and organizing the various files.
She had often done this since Yui Ikari's resurrection. Aside from that, little had changed.
The few people who knew the truth understood that she was hiding her sense of loss.
In truth, Ritsuko had once fallen in love with Gendo Ikari...
And she was not the only one. Her mother, Naoko Akagi, had as well.
Before NERV was founded, Naoko had developed the biological computer MAGI.
To do so, she had implanted her three personas into it.
(Who knew where Gendo Ikari got his charm... enough to leave both mother and daughter utterly infatuated.)
To exploit Naoko, Gendo Ikari had even betrayed Yui Ikari in terms of RT...
Ritsuko, still young at the time, had witnessed it herself.
Later... once Naoko had outlived her usefulness, she fell into Gendo Ikari's trap. Through his machinations, Naoko killed First Rei Ayanami, whom he had deliberately sent to provoke her, then took her own life.
Afterward, perhaps out of an unconscious desire to feel closer to her mother, Ritsuko fell in love with Gendo Ikari despite knowing that he was involved in her mother's death. She also became a scientist at NERV, overseeing the MAGI and EVA projects.
She had always wanted Gendo Ikari's attention.
Yet... after Ultraman resurrected Yui Ikari, she saw Gendo Ikari abandon everything and rush to Yui, apologizing even as Yui slapped him. She saw him willingly endure a thorough beating because the one beating him had promised to resurrect Yui.
At last, she saw Gendo Ikari for who he truly was. There was nothing in his heart except Yui Ikari.
He had used both