Timeline #8: RRR II (Rei's Rightful Reasoning)
NERV Headquarters, Central Dogma, moments before the first Rei Ayanami encounters Naoko Akagi...
*Ding!*
"Perhaps...given how upset the Sub-Commander became when the Commander started saying bad stuff about old people, maybe I shouldn't tell the scientist lady what the Commander really thinks of her..."
Thus, the first Rei Ayanami did not pass along Gendo Ikari's spiteful 'old hag' comment to its intended recipient, Dr. Naoko Akagi; as a result, both she and Rei lived. Rei ended up actually becoming friendly with Naoko, and thus less 'robotic' in her behavior due to her now having a female role model in her life. Sometime later, Gendo accidentally let slip what he really thought of Naoko, and this, combined with his neglectful 'parenting' of Rei, led to an infuriated Naoko 'accidentally' arranging for one of the MAGI-controlled elevator cars in NERV headquarters to malfunction and swiftly plummet to the bottom of the shaft with a *CRASH!*...while Gendo was still inside it. She would then use her knowledge of NERV HQ's information and surveillance systems to cover up the incident and blame it on shoddy construction and engineering.
Kozo Fuyutsuki was soon promoted to Supreme Commander of NERV, with Naoko taking his place as Sub-Commander. She would learn of Rei's origins, but due to having grown fond of the girl, decided to let her live, and Rei ended up being raised jointly by both herself and Fuyutsuki. Naoko would then remember Gendo's son, Shinji, and on feeling sorry for the boy who was now effectively an orphan (also guilty for having had a hand in the demise of his father, for one thing), along with wanting Rei to have a friend her age, arranged for Fuyutsuki to introduce the two, with the former professor presenting Rei as a distant, orphaned relative of Shinji's mother who had recently come into his care. Shinji and Rei became good friends, and eventually Shinji moved to Tokyo-3 permanently.
On seeing a happy Shinji and Rei playing together, Naoko and Fuyutsuki turned on SEELE, beginning with Naoko falsifying an order to have the embryonic form of Adam shipped to NERV-Central for testing. Due to its close resemblance to a normal human embryo, she was able to switch it out with that of a soulless Rei clone, sealing it in Bakelite and sending it back to the German NERV branch, with SEELE none the wiser. The real Adam, meanwhile, was then promptly destroyed, which unexpectedly prevented any of the Angels from appearing at all.
Since the Angels never showed up, SEELE never had an excuse to deploy Tabris the 17th Angel, and once the allotted time passed for the Angels' prophesized arrival with no sign of them anywhere, the conspiracy turned on itself as SEELE lost control of the world's governments. Said governments, in turn, could no longer tolerate footing the bill for a bunch of giant robots built for a war that never started, and couldn't function for more than five blasted minutes, making them useless for normal, human-based conflicts. Consequently, NERV was shut down, the Evangelions were decommissioned, Yui Ikari and Kyoko Zeppelin Sohryu were freed from the cores of Units-01 and 02, and just before the Geofront was sealed up for good, Fuyutsuki and Naoko oversaw the operation that had Lilith the Second Angel dissolved with a powerful acid, destroying the ancient eldritch abomination once and for all.
To the next timeline...