These three episodes (21 thru 23) are the lead in to the end. Even as SEELE's plans approach fruition both Rei and Asuka are subjected to bruising attacks. New themes are introduced, some questions are answered, and we begin to understand that Gendo Ikari's agenda is to be a god maker - the herald of a new existence.
1) The Birth of NERV
In the aftermath of Unit 1's actions SEELE begins an intensive investigation into Gendo Ikari's actions. This culminates in suspicion turning on Ryoji Kyogi. Misato's heartbreak is played against the story of the beginning of Gehirn, the project that was to become NERV. For the first time we learn of Shinji and Rei's beginnings. In addition, we learn what Rei has always known - the EVA's are far more than dolls.
2) At Least be Humane
Asuka, worn down by her repeated losses of self esteem, begins to lose the ability to synchronize effectively with Unit 02. This leaves her vulnerable when Angel 15 (Arael) takes position on orbit where the EVA's cannot reach it. In an eerie episode, Asuka and her EVA are hit with a psychic attack that frays away at her fears and threatens to destroy her personality. Rei must attempt a rescue with the Lance of Longinus, but terrible damage is done.
With Asuka in tatters and Unit 01 untrustworthy only Rei can take active duty when Angel 16 (Armisael) attacks. The angel invades Unit 00 in an attempt to mesh. Rei finds herself forced into introspection that she isn't used to. Unable to stop the angel Rei chooses self-destruction. Even though Rei seems to survive, something is wrong and Ritsuko's guilt leads her to reveal more about the project to Shinji and Misato.
One of the interesting themes that are introduced is that of motherhood and family. All of the characters share some sort of deep injury in their core relationships. In addition, we discover that Rei is somehow related to Shinji. Perhaps, in Gendo Ikari's mind, she is in some way a substitute for Yui Ikari (Shinji's dead mother). In these layers of misplaced emotions, there is no promise of healing. Instead, with the appearance of the Lance of Longinus pinning the second angel in a mock crucifixion, the play of spiritual imagery reached a new peak. Death and transformation is the path offered, as if the only way to recover is to become something more - or less - than human.