Shinji Ikari, a 14-year-old boy in the city of Tokyo-3, is delivered to the secret organization NERV, where he is requested by his enigmatic father to save the city from an invading creature called an Angel.
In the wake of the previous battle, Misato hastily decides to let Shinji have a room in her apartment, where he discovers just what an irresponsible person his new guardian is. Shinji is also haunted by memories of his fight with the Angel.
Shinji transfers into a new school within Tokyo-3, catching the fascination of his classmates - and igniting the ire of one student whose sister was injured in the EVA's last battle. Meanwhile, a second Angel makes its way into the city.
Frustrated by his newfound responsibilities, Shinji runs away from Misato and NERV. After being escorted back to the organization by armed officials, Shinji must decide whether he truly wants to abandon his role as a pilot.
Rei Ayanami, the pilot of Evangelion Unit 00, is scheduled to undergo another activation test following a horrible accident nearly a month earlier. Shinji makes attempts to understand Rei and her close relationship with his father.
A new Angel invades, striking a critical blow against Shinji. Taking the enemy's abilities into account, Misato crafts a special strategy involving Units 00 and 01 as well as an enormous positron rifle. Shinji also discovers Rei's motive as a pilot.
A new nuclear-powered military robot, Jet Alone, goes out of control during a demonstration ceremony and heads toward an almost certain meltdown. With the help of Shinji and EVA-01, Misato takes it upon herself to stop its rampage.
Misato, Shinji, Touji and Kensuke travel to a famous aircraft carrier to collect the new EVA-02 and its prideful pilot, Asuka Langley Souryuu. A seaborne Angel strikes the fleet, and Asuka leads Shinji into her Eva's entry plug for an immediate demonstration of her skills.
A quick attack against a new Angel by Asuka and Shinji ends in an embarrassing defeat when the Angel suddenly divides itself. Shinji and Asuka undergo learning a series of synchronized dance movements as per a new team-oriented strategy.
Banned by Misato from going on a class trip to Okinawa, Shinji and Asuka catch up on their studies. An embryonic Angel is found inside a volcano, and Asuka volunteers to carry out the perilous task of retrieving the creature.
A city-wide power outage puts NERV into a crisis as another Angel invades Tokyo-3. Shinji, Rei and Asuka attempt to make their way into the headquarters as NERV personnel ready the Evas for manual deployment.
Misato is promoted to the rank of Major, but she reveals her long-buried sentiments concerning her work at NERV. A massive Angel appears in Earth's stratosphere, and all three Evangelions are deployed to stop it.
During a simulation plug experiment, an Angel with the ability to mimic computer circuitry manages to invade the MAGI supercomputer system and trigger a self-destruct sequence. Ritsuko delves into the system's inner workings and leads a furious attempt to cancel the process.
The Human Instrumentality Committee recollects the past Angel encounters and battles while Gendou conceals the matter of the recently discovered virus-like Angel. Rei and Shinji undergo inter-compatibility testing with their respective Evangelions, but this experiment culminates in a strangely familiar incident.
Shinji visits his mother's grave in the company of his father, and Misato reflects upon her bygone romance with Kaji. Soon afterward, Kaji and Misato discover a startling secret within NERV's Terminal Dogma.
A bizarre Angel possessing a spherical shadow in the air and a Dirac sea-type body on the ground absorbs Shinji and EVA-01. While NERV searches for a means of destroying the Angel--even if that means killing Shinji as well--Shinji languishes inside the entry plug, pondering his role as a pilot and his relationship with the people in his life.
As EVA-04, the planned testbed for the S² engine, disappears under mysterious circumstances, NERV quickly prepares the testing of EVA-03 and the selection of its pilot. Shinji and Touji continue to bond, and Hikari begins to emotionally open herself to Touji.
The activation of EVA-03 goes awry when an Angel takes control of the unit. With EVA-03 itself re-designated as an Angel, Shinji is faced with the moral dilemma of terminating the rogue Evangelion at the risk of harming or killing the pilot trapped within.
Shinji, furious at his father for the orders given in the previous battle, resigns from NERV. But as an Angel lays waste to the Geo-Front and the other Evangelions, he begins to reconsider his hasty decision.
His physical form absorbed by EVA-01, Shinji drifts through an introspective state, again contemplating his "mission" and role as a pilot. Meanwhile, Ritsuko and NERV desperately attempt to recover him.
As Kouzou is interrogated by SEELE, he reminisces about the history of NERV, its parent company GEHIRN, Yui and Gendou Ikari, and Ritsuko's mother Naoko Akagi. At the same time, a horrible fate is in store for Kaji concerning his shadowy dealings.
Asuka, haunted by childhood memories of her mother's suicide and a notion that she "lost" to Shinji in the previous battle, begins to lose her precious self-confidence as a pilot. A new Angel appears in space and invades Asuka's psyche through a strange beam of light, rendering her helpless.
When an Angel resembling a coil of light arrives, Rei and Shinji are sent to battle it, but the assimilating ability of the foe prompts Rei to self-destruct the EVA-00 in order to kill it and save Shinji. Mysteries abound as a clone of Rei later appears in the hospital, and Ritsuko reveals the terrible secret of the "dummy plug" system to Misato and Shinji.
A despondent Shinji encounters a kind-hearted boy named Kaworu, who quickly becomes his close friend. However, Kaworu (selected earlier as the replacement pilot for EVA-02) is soon revealed to be the final Angel. This turn of events leaves Shinji with a cruel dilemma: saving humanity will mean he must kill his only true friend in the world.
Shinji, pained by his choice to kill his friend Kaworu, shuts himself off from the world and the people in his life and reflects upon what his true purpose in life is. Instrumentality begins as Shinji wishes for a world of complete solitude and seclusion.