episode
21: He Was Aware that He was still a Child
This episode puts some of the missing puzzles pieces together in the series by using a string of flashbacks. We find out that Gendo's real name was Gendo Rubunki back then. We also find out how Gendo met his future wife Yui Ikari in college and that her professor was none other than Fuyutsuki himself. Yui was working for SEELE when she married Gendo and had Shinji. Later on in the flashback, Gendo brings Fuyutsuki to and underground cavern where we see Naoko Akagi (Ritsuko's Mother) still developing the MAGI computers, which will eventually be a necessary factor in the fight against the Angels. Yui and Gendo also show Fuyutsuki Eva 00 prototype, which was made from Adam and will eventually be the blueprint for the other Evangelions. Yui dies, leaving young Shinji to his father, who then abandons Shinji to his relative and Sempai (teacher). Naoko doesn't seem saddened by the mishap that just occurred. Further in the flashback, Gendo introduces a child named Rei Ayanami (who looks very similar to Yui right down to her hair style, body, and even the number of letters in her name), saying that she is a child of someone he knows and that he is only taking care of her for that person. Gherin (the project Gendo used to lead) is disbanded and NERV takes its place. In the end you see naoko strangle rei to death and then commit suicide.