Timeline #9: Gendo Ikari's Gratefully Good Ending
2004, Tokyo-2 rail station, moments after Gendo and Shinji had arrived from Tokyo-3...
*Ding!*
"Wait, what am I doing?! I nearly turned into my parents just now-abandoning my own son like they did me! I've got to go back for Shinji-especially since, even if I succeeded and brought her back, Yui would probably kill me for even thinking of sending Shinji away!"
Gendo Ikari, not wanting to repeat his own personal history, thusly did not abandon Shinji, instead taking him for a little day trip into Tokyo-2, where Gendo slowly, but surely, began to foster the bond between father and son. When Rei Ayanami was accidentally created in his attempt to bring Yui back, Gendo took the clone girl in as his own, giving Shinji a little sister in the process. Now having become something of a family man, he abandoned his plan to manipulate Naoko Akagi, politely turning her down when she made a romantic overture towards him. Consequently, following a bit of a drinking binge in response to this rejection, Naoko, after gathering her thoughts, instead started something with Kozo Fuyutsuki.
Spending time with his children eventually made Gendo truly realize that life was worth living, even without Yui, and in wanting to ensure a better future for Shinji and Rei, he, together with Fuyutsuki and Naoko, exposed the SEELE council and their conspiracy. Incidentally, their actions came just before the German branch of GEHIRN had finalized the test conditions for Evangelion Unit-02, and once they learned of what their backers in SEELE had planned, the German branch's lead scientist, Dr. Kyoko Zeppelin Sohryu, called off the contact experiment for the EVA indefinitely, sparing her daughter, Asuka, the horrors of what would have entailed.
A few years later, after the SEELE scandal had been dealt with, while visiting Fuyutsuki and Naoko, Gendo met and became interested in Naoko's daughter, Ritsuko; the two began a relationship following that. Naoko, having grown happy with Fuyutsuki (and on a subconscious level, eager for grandchildren), decided to cast aside her initial jealousy over her daughter romancing her former love interest, guaranteeing that Ritsuko would find happiness as well.
To the next timeline...