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Shinji Ikari is summoned to NERV by his cold father, Gendo Ikari, who tells him he has a use for him. At the same time, a giant being known as an "Angel" also arrives in New Tokyo-3, which is met by the ineffectual offense of the U.N. Shinji must pilot the equally giant Evangelion Unit-01, but at what cost?
The city is saved and clean up and rebuilding begins. Now needing a place to stay, Shinji is taken in by the beautiful Misato Katsuragi who has presided over him since his arrival. They begin their awkward relationship joined by the hot spring pinguin Pen Pen, while Shinji's memory of battling the Angel comes crashing back.
A heavy regimen of training inside Unit-01 begins, and more secrets about "Second Impact" and the Angels are revealed. Shinji starts his first day at a new school and meets two classmates whom will become good friends. The Fourth Angel arrives, and a rage-filled Shinji goes against orders to defeat it.
Shinji runs away from Misato and NERV after hurting each other in their attempt to be closer. Their relationship is described as the "hedgehog's dilemma," wherein the closer they become to more they can hurt each other. Shinji si finally captured by NERV and discharged, but his need for others keeps him from boarding the outbound train.
Rei Ayanami begins the second activation experiment with Unit-00 after a disastrous activation 22 days previously. Much like Gendo, she displays little emotion, even after being seen naked by a flustered Shinji. Study begins on the fallen Fourth Angel revealing its DNA to be identical to humans.
Eva-01's first encounter with the fifth Angel goes badly. While Shinji heals, Misato displays her tactfulness by organizing Operation Yashima, which involves utilizing all the electrical power in Japan to power a prototype rifle. The success hinges on the teamwork of both Eva-00 and Eva-01.
The mystery around Second Impact and the Evas is partially revealed. Misato and Ritsuko head off to see the activation of the pilot-less robot Jet Alone. However, the giant nuclear powered robot mysteriously runs amok, and it's up to Misato and Shinji to stop it before it melts down.
Misato along with Shinji and his classmates Toji and Aida fly to a navy battle group, which is transporting the newly assigned production model Eva-02. The group meets the new pilot, the spirited Second Child Asuka Langley Sohryu, before the sixth Angel appears.
Asuka and Shinji face off against the seventh Angel, which ends up being able to split into two halves. Their only way to defeat it is by vigorously training to perform a perfectly synchronized ballet-like attack.
The three Children take time off at a NERV pool, where Asuka teaches Shinji about thermal expansion. Inside the volcano Mt. Asama, the eighth Angel is discovered in its larval form. Eva-02, outfitted with Type-D armor, is sent deep inside the magma to retrieve it before the Angel can hatch.
The day starts off with everyone doing normal chores, but things are cut short when the power mysteriously goes out in Tokyo-3. The three Children must find their way back to headquarters with the over-confident guidance of Asuka. While Hyuga is in the city above, he hears from a U.N. plane flying overhead that another Angel is approaching and makes his way to NERV to start the manual activation of the Evas.
A flashback to the Second Impact shows a young Misato being placed into an escape capsule as the area is decimated. Back in the present, Misato is promoted to Major, which prompts Kensuke and Toji to throw a party. The 10th Angel is detected high above Earth's atmosphere zeroing in on Tokyo-3, where it will fall and collide directly.
Ritsuko begins running a series of diagnostics on the three MAGI supercomputers, afterwhich she tests the Eva pilots who must be nude inside simulation Evas. Some corrosion is detected during the test that ends up being the 11th Angel. The pilots and Evas are ejected from the area as the Angel infects the computers and almost takes over the MAGI, forcing Ritsuko to battle the Angel with the MAGI computer Casper.
The members of SEELE hold a meeting to go over the events that have happened so far, recapping the encounters with each Angel. They give Gendo a warning about following their plans using the Dead Sea Scrolls. Ritsuko performs another test by having Rei inside of Unit-01 and Shinji inside Unit-00, but Unit-00 goes berserk.
Kaji makes a trip to Kyoto for a secret meeting, as Asuka goes out on a blind date and Shinji and Rei stay after class to clean up. The next day Shinji visits the grave of his mother with Gendo, the first time in 3 years. Misato, Ritsuko and Kaji attend the wedding of a friend and reminisce about their past, while Asuka and Shinji find something to pass the time.
While going through another series of synchronization tests, all three Eva's are launched when the 12th Angel makes its appearance. Conventional weapons prove useless as Unit-01 sinks into the Angel's shadow. After much research Ritsuko calculates Shinji is inside a "Sea of Durac" in the Angel, but destroying it is almost impossible. Shinji begins to slip into unconsciousness as the life support systems run out of power.
Misato is interrogated by SEELE about the latest encounter with the Angels. It is learned the second branch of NERV in Nevada has vanished when a prototype S2 engine was installed into Eva Unit-04, after which the U.S. government request to transfer Unit-03 to the Japanese branch. Toji and Shinji make a trip to Rei's apartment to bring some school papers, while the fourth pilot of Unit-03 is chosen.
As Eva Unit-03 is flown into Japan, Misato and Ritsuko await its arrival. Kaji is left to take care of Shinji and a distraught Asuka while Misato is away. With the reluctant Fourth Child aboard, Unit-03 goes berserk during a routine test, causing a giant explosion at the remote testing facility. Reclassified, the thirteenth Angel easily disables Asuka's and Rei's Evas leavin gthe fate of the Fourth Child in Shinji's hands.
After the traumatic events within the thirteen Angel, Shinji refuses to leave Unit-01, forcing Gendo to render him unconscious. Vowing to never pilot again and facing criminal charges, Shinji leaves NERV once again. His departure is cut short by the arrival of the most power Angel yet. Despite a valiant effort, Asuka and Rei are defeated, forcing Shinji to decide what is most important to him.
The aftermath of the last Angel attack has left NERV and the Evas completely disabled to the dismay of SEELE. But while Rei and Asuka are safe, Shinji has disappeared inside his Eva. It is believed he is still alive in a different form, and Ritsuko uses all of her experience to come up with a way to save him. Shinji awakens in his new form, and as time passes, the Eva is repaired, and Ritsuko prepares the salvage operation.
Vice-Commander Fuyutsuki has gone missing, and Misato is held captive with Kaji as the prime suspect. Fuyutsuki is being questioned by SEELE, who recounts his first involvement with Yui Ikari and Gendo Rokubungi and the events afterward. The histories of Misato, Ritsuko and Professor Akagi are also recounted.
A flashback shows Asuka as a child and the death of her mother. In the present her synch ratio is falling to the concern of Ritsuko and Misato. She takes out her frustration on Rei in an elevator while her synch ratio continues to drop. Another Angel appears above Earth's atmosphere and begins to attack Asuka in Unit-02 directly through her mind.
As Misato mourns the loss of Kaji, Asuka becomes more withdrawn from the world. The sixteenth Angel shows up and Rei is launched to fight it, but when Shinji arrives to help, she makes the fateful decision to self-destruct to save him. SEELE reveals that only one Angel remains, while Ritsuko shows Misato and Shinji the dark secrets of NERV.
Shinji is depressed over the ruin of Tokyo-3 and all his friends who have left. A boy appears nearby who reveals himself to be Kaworu, the fifth Child. They become close friends as Kaworu excels at synch ratio tests. But as suspected, Kaworu is the final Angel and takes control of Unit-02, with Shinji as the only one who can save humanity from being destroyed.
With the final Angel destroyed, Shinji struggles with his decision to kill Kaworu. He ponders why he pilots Eva; is it for the sake of mankind or simply to receive sympathy from others? Disappearing into nothingness, Gendo tells Shinji that this is simply the return to the state of the beginning, the primal womb that was lost. Misato tell shim this is Instrumentality, and Shinji's wishes have shaped the world into a place of nothingness.
As Instrumentality continues, Shinji feels he can disappear from existence because he is unwanted. Without piloting Eva, he is useless, without an identifier. Now in a world of nothingness, with no restrictions, he can do anything, but without others he has no identity. After a glimpse at one possible existence, he realizes the way the world is seen can change through different perceptions and that there could be value in living.
A flashback shows Asuka as a child and the death of her mother. In the present her synch ratio is falling to the concern of Ritsuko and Misato. She takes out her frustation on Rei in an elevator while her synch ratio continues to drop. Another Angel appears above Earth's atmosphere and begins to attack Asuka in Unit-02 directly through her mind.
