This is an expansion of something that I had in the crossover twists section of the miscellaneous folder.
This would take place after the end of Noir, and some time after the arrival of Asuka on the NGE side (Whether Kirika is a pilot instead of or along with Touji is something I'm leaving open).
Shinji Ikari spent his early childhood with his parents and his twin sister Kirika. He was totally unaware of the fact that a woman named Altena had visited his sister she was a baby, and blessed her as worthy of taking up an ancient fate. The implications of this would not become clear until after the two siblings watched their mother disappear during a test at a GEHIRN research facility.
Shortly after that, Shinji's father turned him over to the custody of an uncle, claiming that he had no use for the boy. Despite Shinji's pleas, Gendo would not let Kirika go with him, as she was still useful to her father. After Shinji was sent away, Kirika was turned over to Altena, to be trained to become an elite assassin, one who would be tested as a candidate for the title of Noir.
Years later, Shinji is called back to his father's side. When he does, he finds that Kirika is not there. Asking around, he finds that nobody at NERV remembers her ever being there, or even knew that Gendo had a daughter in the first place. Apart from one photograph that Shinji kept, all evidence that Kirika ever existed has vanished without a trace.
Some time after the arrival of Second Child Asuka Soryhu, a Fourth Child is found in Paris and sent to Tokyo-3. The Fourth Child is named Kirika Yumura, and with her comes her guardian, Mireille Bouquet. Shinji finds the new pilot to be extremely familiar for some reason, and after a test that showed that she could also synch with EVA-01, manages to convince Ritsuko to do a DNA test - and finds that the new pilot is his missing sister (someone who by now most of NERV was willing to believe was a figment of Shinji's imagination).
The discussion between Ritsuko, Shinij and Kirika after the discovery is made is rather unusual. Kirika has no memories of her early childhood. She categorically refuses to discuss her later childhood for any reason. She also is against forming connections with other people unless necessary, so as to avoid the pain of losing them. Shinij has found his sister, but she is a total stranger to him, and vice versa (After learning about this, Gendo's relationship to Kirika remains the same: an unspoken agreement between the two to ignore each other outside of work-related issues).
Asuka has misgivings about the Baka's twin for totally different reasons. One day, after leaving school late due to drawing cleaning duty, she and Kirika were attacked by fanatics who believed that the Angels were messengers of God and that therefore EVA was a tool of the devil. Before Section 2 even noticed that the pilots were in danger, Kirika had killed one of them with her student ID, taken his weapon, and used it to kill the others. Asuka doesn't want to know WHO Kirika is, she wants to know WHAT she is, as people who can kill that swiftly and casually aren't exactly common.
Meanwhile, the thousand-year-old conspiracy known as Soldats is unhappy. Two of the three selected candidates managed to complete all the trials to become Noir, the legendary enforcers of the Soldats. However, instead of swearing fealty to High Priestess Altena and becoming the tool with which Soldats could shape the world, they killed Altena and the entire priesthood and opted to remain as freelance assassins. Noir is willing to do jobs for Soldats, but only on the same terms with which they do business with every other client (Which includes the right to decline a contract).
They also have to worry about SEELE, a fledgling conspiracy that nevertheless has acquired considerable power and threatens to supplant Soldats' supremacy. The fact that Noir is willing to do business with SEELE on the same terms that they do business with Soldats doesn't help.
With Noir relocated to Tokyo-3, and control of the SEELE-sponsored organization NERV given over to a minor Soldats member named Gendo Ikari, Soldats starts developing a plan to put the newcomer into its place.
SEELE, on the other hand, believes that Gendo is their man planted into Soldats, and starts developing a plan to ensure that Soldats cannot interfere with the Human Instrumentality Project. This plan also involves the services of Noir, though they do not know who Noir really is (As Gendo never thought to ask WHY Altena wanted his daughter).
Whose side is Gendo on (besides his own)? Which conspiracy will win? Will Shinji get his sister back? How will Asuka react when she finds out what her roommate's sister does for a living? How will Shinji react, for that matter? And what will be the effect of having a pilot trained to kill, rather than trained to pilot mecha, have on the war against the Angels?



