Seeing the wounded pilot being pulled from the Unit 03 wreckage to be Toji is too much for Shinji to cope with, as a result Shinji's mind finally lets go and almost snaps. He refuses to leave the cockpit of Unit 01, starts threatening to level NERV with the remaining battery power he has available to him and almost goes so far as to telling his father face to face that he hates him. In the end Shinji is forcedly removed from the cockpit as ordered by an impatient Commander Ikari who Shinji later finds himself answering to. Though instead of confronting his father and letting go of his anger, Shinji chooses again to run away and resigns as the pilot of Unit 01.

Fortunately Toji recovers and is visited by Hikari Horaki, supposedly the concerned class representative of class 2-A, but there's more to her visit than mere concern. Hikari has recently become extremely fond of Toji, however, she still can't seem to find the right time to express her feelings towards him.

The fourteenth Angel, Zeruel, arrives along with all its destructive power intent on reaching Adam in terminal Dogma. With one shot it's able to penetrate eighteen layers of the defensive armour plating surrounding the geo front. Due to the Angels awesome power, Misato has Asuka intercept the Angel directly in front of NERV HQ, however, despite Asuka's valiant effort in trying to stop the Angel, Unit 02 is completely ripped apart and its head sent crashing into the nearest shelter. Unable to synchronise with Unit 01, Rei goes out in Unit 00 minus one arm. She takes with her an N2 mine and attempts to penetrate the Angel's AT field blowing it to hell and back. Unfortunately Rei fails.

Having not yet left, Shinji witnesses the whole horrific battle. Unable to sit back and watch as his friends are mercilessly butchered, coupled with a few words from Kaji, who for some reason is out watering melons whilst everyone else is busy evacuating, Shinji races back to NERV demanding to pilot Unit 01. As the dummy plug fails to respond, NERV send out Shinji in Unit 01, but they couldn't have predicted the events to come as Shinji achieves a synchronisation ratio of four hundred percent finally awakening the savage Eva beast.

Genesis 0:10/Episode 20 - Form Of The Mind, Form Of The Man

With the savage Eva beast of Unit 01 now fully aware, it starts to mercilessly devour its fallen opponent; the fourteenth Angel, and in doing so takes the Angel's S2 engine into itself. It then starts tearing off its armour, which was installed by NERV purely to contain the Eva binding it to their will thus allowing them to control it. With these restraints now partially removed, NERV find themselves facing the possibility of their own creation, or rather their adapted copy, running wild in side the geo front.

Fortunately NERV are able to freeze the Eva allowing them to work on repairing it whilst in stasis. Also both Units 00 and 02 sustained serious damage during the Angel's onslaught and as for the pilots, whilst Asuka and Rei survived the incident, Shinji still remains trapped inside Unit 01. With NERV HQ partially destroyed and part of central Dogma exposed, NERV decide to temporarily move location to their secondary control centre where they can continue to operate. Of course none of this was in accordance with SEELE's, otherwise known as the UN committee, predictions and the committee becomes somewhat disturbed by the recent events.

Unable to get Shinji out of Unit 01's entry plug, Ritsuko's staff engage the plug's internal monitors allowing then to check on Shinji's status. But when the monitors reveal the plug to be empty, Ritsuko finds herself admitting to the truth behind the four hundred percent synchronisation ratio, and the fact that it's not the first time that an accident like this has occurred. She reveals that the first time this exact incident occurred was during her mother's era, and that the pilot underwent some form of change due to the LCL, Link Connection Liquid, in the plug.

Although the late Naoko Akagi, Ritsuko's mother, came up with a way to recompose the pilot with the MAGI's support, their rescue attempt was unsuccessful and the pilot's soul lost within the Eva, however, Misato isn't just about to give up on Shinji and so the operation goes ahead. But when all's said and done, Shinji can only return to his material existence if he wants to. Though considering what he's been through recently, this may well not be the case.