The Angels have returned with their third messenger of death, Sachiel, who is laying waste to Tokyo-3, home to NERV HQ, and the feeble resistance put up by the entire UN force present. All of which, however, proves to be of no avail, even the devastating power of the UN's latest addition to their arsenal, the N2 non-nuclear mine, proves to be laughable when faced with the wraith of the Angels. As a result of the UN's ineffectiveness, command of the defence operation is transferred to NERV.

NERV respond to the dire situation by preparing the launch of mankind's last hope for survival; Evangelion, a bio-mechanical giant specialising in close combat and capable of generating its own AT, Absolute Terror, field. EVA-01 is ready, all that NERV require now is a pilot. Only children born in the aftermath of the second impact, exactly nine months after the massacre, have the ability to synchronise with an Evangelion and thus pilot it. The first child was found and underwent the process of synchronising with her Eva, however, the doomed test pilot, Rei Ayanami, lost control of her prototype Eva, EVA-00, in a mysterious accident which left her seriously injured.

All is not lost, however, as a potential new pilot is found, the third child Shinji Ikari, estranged son of Gendo Ikari; Commander and head scientist at NERV. Shinji is picked up by Captain Misato Katsuragi on the day of Sachiel's attack, however, both are caught up in the cross fire between the Angel and the UN whilst enroute to NERV HQ. Fortunately though both Shinji and Misato make it through with only a few scratches and Shinji is brought before his father for the first time in three years.

Despite his reluctance to pilot EVA-01, Shinji finds himself being railroaded into synchronising with the Eva having been alerted to backup pilot Rei's critical condition. The synchronisation process between Shinji and EVA-01 goes surprisingly well, Unit 01 is activated and the battle for Tokyo-3 is set.

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.

It's been twenty two days now since the pilot of the Eva prototype, EVA-00, mysteriously lost control of her Eva during her first attempt to synchronise with the Unit. Twenty two days since Rei was seriously injured, despite having been rescued by commander Ikari who opened the super heated hatch on Rei's entry plug with his bare hands, a courageous action which left his hands permanently scared. Now Rei is preparing herself to re-undergo the synchronisation process with Unit 00.

Ritsuko heads up the salvage operation for the fourth Angel which, due to the manner in which the Angel was disabled, NERV have been fortunate enough to obtain as it's a near perfect specimen for which to study. Analysis of the Angel reveals its structural composition, although being composed of different matter, to be almost identical to that of humans. Whilst Ritsuko and Misato analyse the data, Shinji notices the scaring on his father's hands whilst he examines the Angel's corpse. Misato arrived at NERV after the incident with the prototype Eva, however, Ritsuko knows all to well the events in question and agrees to fill Shinji and Misato in on the details.

Later that evening, having agreed to join Misato and Shinji for dinner, Ritsuko gives Shinji Rei's new security card to pass on. Apparently Ritsuko's forgotten to pass on the card in person, at least that's the story, and so Shinji gets the job, along with an excuse to go over to Rei's place. The following day Shinji takes the card over to Rei's, however, it doesn't quite go as planed when the third child manages to elegantly end up on top of a naked Rei on her bedroom floor. Matter aside though, the two of them proceed together to NERV HQ where Shinji discovers that Rei appears to have the kind of relationship with his father that he has always longed for.

The fifth Angel, Ramiel, arrives in Tokyo-3. As the successful synchronisation between Rei and Unit 00 has only just been completed, it's decided that Rei is still unfit to fight and so Shinji in Unit 01 is launched. With little or no data on the new Angel, however, this soon proves to be a huge mistake.

Spending so much time around the sisterly Misato is starting to have an influence on Shinji's behaviour, he's now become accustomed to her ways, is starting to express his feelings more freely and has even gained a little self confidence. Again Toji and Kensuke arrive that morning with the hope of catching a glimpse of Misato before they and Shinji, who can't understand their love towards Misato, head of to school.

Whilst sitting in the cockpit within Unit 01's entry plug during routine tests, Shinji becomes distracted with his past experiences with Eva and finds himself questioning Eva's existence. Later Ritsuko reveals the truth behind the second impact, in that a mere meteorite striking Antarctica wasn't the cause. She states that man discovered the first Angel in Antarctica and that this discovery lead to the second impact caused by the Angel. After the disaster NERV was established to prevent a probable third impact and knowledge of the Angel's existence was covered up, Misato still, however, isn't convinced that NERV's definition of the truth is to be trusted.

On behalf of NERV, Misato and Ritsuko attend the initial activation of the Jet Alone project, an intended low budget replacement for project Eva. The creators of the potential Eva substitute boast its one hundred and fifty days of continuous power supplied by an on board nuclear reactor, however, Ritsuko is far from being impressed with the idea of a walking nuclear bomb.

NERV's scepticism is soon proved well justified as the activation of the Jet Alone unit goes horribly wrong. It fails to respond to the commands of its creators, which leads to the monster walking through the observation building intent on heading towards the centre of Tokyo. With nuclear melt down imminent, the unit out of control and failing to respond, Misato soon finds herself heading up an operation to prevent the destruction of the city. As ordered by Misato, Shinji piloting Unit 01 is flown in to carry out her plan, that is Shinji will place Misato on the Jet Alone and attempt to restrain it whilst she dissables the machine manually from within. Misato is soon in for a surprise, however, as Jet Alone's on board computer rejects its password meaning only one thing, sabotage!

It would seam that Asuka is proving to be quite popular amongst Shinji's classmates, however, he, Toji and Kensuke know better having had to put up with her constant arrogance during their last Angel encounter, but it's not a complete loss. Fortunately for them Asuka's photos don't reveal her personality, meaning a further source of income for the three. Whilst Asuka attends her first day at a Japanese school, Kaji is shamelessly attending to his own personal interests. Having given up the doomed battle to rekindle the flame between himself and Misato, he's now taken a shine to Ritsuko much to Misato's annoyance.

The seventh Angel, Israfel, is making its way towards Tokyo-3, however, due to recent damage incurred to the city's intercept system, NERV are forced to engage the Angel at the water's edge just before it reaches land. It is also decided to launch Units 01 and 02, much to Asuka's dislike, to limit further damage to the city. Both pilots are soon in for a shock, however, when they discover the Angel's ability to duplicate its self. Consequently both pilots, unprepared, confused and unwilling to co-operate together, loose the confrontation in an embarrassing manor and so NERV are forced to withdraw and rethink their plan of attack.

Fortunately the damage caused by Unit 02 and the N2 mine detonated on the Angel by the UN buys NERV some time whilst it regenerates. NERV have six days until the Angel fully regenerates and resumes its attack on Tokyo-3. Misato therefore has Asuka stay with her and Shinji in order to get them to co-operate before NERV implement their second attack on the Angel, however, the process of getting Asuka to work with Shinji turns out to be a tricky one, not to mention embarrassing.

Day six finally arives and as predicted the Angel resumes its attack on the city, now Asuka and Shinji must put aside their differences and work together for NERV to stand any hope of defeating the Angel.