With the latest Angel confrontation adding further to the extent of damage to Tokyo-3, all of Shinji's classmates leave, along with most of the city's inhabitants, for the fear of loosing their lives. To add to Shinji's loneliness, Asuka goes missing, and Misato continues to shut her self off from the outside world. The only person that Shinji can still talk to is Rei, but this soon changes as the sixteenth Angel, Armisael, arrives.

NERV send in both Units 00 and 02, now having tracked down Asuka, again Unit 01 is held back as ordered by Gendo. The latest Angel has the ability to change its form at will, and as a result of this is able to outmanoeuvre and come into direct contact with Unit 00, where upon it starts to merge with the Eva. The Angel's invasion of Unit 00 proceeds at a frightening rate, and when NERV learn of Asuka's inability to synchronise with her Eva due to her current mental state, Gendo is left with no other choice but to sortie Unit 01, however, this action doesn't help at all as the Angel is just too agile for any Eva to combat. Unwilling to allow the Angel to merge with Unit 01, Rei initialises Unit 00's self destruct sequence whilst remaining in the Eva maintaining its AT field, that is its grasp on the Angel. The Angel is destroyed, the mission completed though at a price, Unit 00 is lost and Rei is killed.

It is later revealed that Rei was in fact not killed, however, she now seems like a completely different person. What with the loss of Unit 00 as well as the lance of Longinus and Gendo's newly found God, Unit 01, SEELE mark the beginning of the end of their fragile relationship with NERV by demanding the pilot of Unit 00 delivered to them, presumably to replace the loss of their last catspaw, Kouzou. Instead though, Gendo sends Ritsuko to be indecently interrogated by SEELE.

Like mother like daughter, Ritsuko learns of Gendo's betrayal of love towards her in that her secret lover saw fit to recreate Rei ultimately proving his ongoing love for Yui. Out of vengeance Ritsuko reveals the truth about Rei to Misato and Shinji, that Rei is in fact the core of the dummy plug system, that Gendo has created multiple copies of her body and how all of which are no more than empty husks. Revenge driven, Ritsuko destroys the entire dummy plug system.

Genesis 0:12/Episode 24 - The Final Messenger

Due to Asuka's inability to pilot Unit 02, NERV plan for the arrival of a new pilot, the fifth child, Kaoru Nagisa. Whilst at the same time Ritsuko finds her self subjected to interrogation whilst being detained for her actions by NERV.

The fifth child arrives and immediately takes a liking to Shinji, however, NERV, in particular Misato, are more than a little suspicious concerning the boy's arrival. Like Rei, all of his past records have been erased, except for one detailing his date of birth, and furthermore NERV determine the fact that he is capable of achieving any synchronisation ratio with Unit 02, even before they reconfigured the Eva for the child.

With Asuka now being treated for depression in NERV's hospital, and the third copy of Rei busy contemplating the reason for her existence, Shinji is now utterly alone. He can't even talk to Misato who has now emmersed herself in investigating NERV aided by information from her late lover, and Ritsuko has disappeared too. Though his loneliness isn't to last as he becomes very close with Kaoru; Shinji inexplicably finds him self talking to Kaoru about his past and what he's been through. In fact Shinji takes an extreme risk, for him that is, in that he places his trust in Kaoru, however, his trust soon turns out to have been well and truely misplaced.

Unit 02 mysteriously activates and starts descending towards terminal Dogma. Asuka is still in hospital though, and the Eva unmanned! NERV soon identify the person in remote control of Unit 02 to be Kaoru, the seventeenth Angel! SEELE have sent the final messenger directly to NERV! Unit 01 is immediately rolled out to prevent the Angel from reaching terminal Dogma, but it's too late as Kaoru breaches the final security seal, thus opening heavens door.

Finally, an Angel reaches Adam, or so it would have been the case were the giant in terminal Dogma actually Adam, not in fact Lilith, that is humanity's mother. Realising this distracts Kaoru, giving Shinji enough time to defeat Unit 02 and restrain Kaoru. Now Shinji must carry out the last wish of his newest friend, an end to life eternal, else let humanity suffer the consequences.