In order to improve his combat skills, Ritsuko's having Shinji participate in simulated training exercises in Unit 01. It would seem though, that Shinji isn't really interest in piloting Unit 01, he simply does as he is told, it seams to be his way of dealing with what life has to offer. This kind of attitude towards life and people in particular is starting to worry Misato.

Shinji turns up for his first day at his new school, however, it appears that most of his classmates have either transferred schools or remained at home due to the latest attack on the city. Toji Suzuhara isn't one of them though, despite having been away for several days caring for his little sister who was injured during the attack and hospitalised as a result. Toji is by far from being impressed with NERV's efforts to protect the city; he blames the pilot of Unit 01 for his sister's current condition.

Word of Shinji piloting Unit 01 soon gets out, which puts Shinji in the spotlight having to deal with all kinds of awkward questions from his classmates, something that he's not accustomed to and finds hard to deal with. Meanwhile war enthusiast Kensuke Aida takes note of Shinji's every word in an attempt to learn more about NERV. Later that day Toji catches up with Shinji, now knowing him to be the pilot of Unit 01, and expresses his anger towards Shinji, but not just in a verbal way.

Last time humanity had fifteen years to prepare for the return of the Angels, now only three weeks since the third Angel's attack the fourth Angel, Shamshel, is headed towards Tokyo-3 resuming the Angels' attack on the city. Knowing this, NERV once again launch Unit 01 to engage the enemy and evacuate the city's inhabitants to the designated underground shelters. They are not, however, prepared for the intervention of Toji and Kensuke, who intend on getting a little closer to the action, and that of the awesome new power displayed by the latest Angel.

Genesis 0:2/Episode 04 - Rain, Escape & Afterwards - The Hedgehog's Dilemma

Misato lectures Shinji after ignoring and going against a direct order issued by her during his last encounter with an Angel. Rather than dealing with the situation though, Shinji chooses instead to escape his problems by running away from them. Having taken the Tokyo-3 loop line, he wanders aimlessly around the city and then up into the foot hills surrounding Tokyo-3 where he unintentionally meets up with Kensuke who's out camping alone. Shinji accepts Kensuke's hospitality and the two talk for quite some time before turning in for the night.

The following morning NERV intelligence agents arrive to pick up Shinji and escort him back to NERV HQ. There he finds himself again having to answer to Misato, however, this time it would seam that she's more or less given up on him. Misato feels that she is unable to help a child who is unwilling to adapt to new situations, if Shinji is unwilling to continue to pilot Unit 01 then forcing him to do so would be a waste of time.

Due to his reluctance to pilot Unit 01, Shinji chooses to leave NERV and is formally dismissed from the organisation. But before heading off to the train station intent on taking the next train out of Tokyo-3, Shinji is caught up by Toji and Kensuke who wish to see him off. Toji regrets his earlier behaviour towards Shinji and apologises.

Now preparing to leave Tokyo-3, Shinji finds himself running away from reality yet again. Misato realises that letting Shinji leave is a mistake and so heads off to the station hoping to catch up with him, but arrives too late only to see the train pull away from the platform. To her delight, however, the train pulls away leaving Shinji standing opposite her on the station's departing platform. They stand opposite each other for quite some time before Shinji breaks the silence with a couple of well chosen words, 'I'm home'. Misato welcomes Shinji back with a smile and the two head back home.