Enter Shinji Ikari, a 14-year-old boy summoned to the fortress city of Tokyo-3 by his estranged father, Gendo. He finds himself lost and alone in the city after its populace had been evacuated, only to find himself caught in the midst of a battle between the United Nations' military and a massive monster. He is saved by the arrival of his attache, Misato Katsuragi, who brings him to NERV, the clandestine paramilitary organization that Gendo leads in the fight against the monsters, known as "Angels".
Within the deepest recesses of NERV's HQ in the subterranean Geofront, Shinji comes face-to-face with the reason he had been summoned: a massive robot-like war machine created to fight the Angels, Evangelion Unit-01. Ritsuko Akagi, a scientist who aided in the construction of the EVAs, instructs Shinji to climb inside. Shinji is too scared to enter the cockpit, however, even with Gendo's goading and Misato's encouragement. Gendo dismisses Shinji and calls for a replacement pilot: Rei Ayanami, a young girl close to Shinji's age who was seriously injured and struggling to even stand.
The Angel begins to blast a path to NERV HQ, causing pieces of heavy debris to fall towards Shinji, only for it to be deflected by Unit-01's hand, which moved autonomously to everyone's surprise. Seeing Rei in pain and bleeding before him, Shinji finally agrees to pilot Unit-01.
The first battle of Shinji and Unit-01 goes disastrously at first, as Shinji struggles to make the Eva walk, falling over and finding himself at the Fourth Angel's mercy. The Angel relentlessly attacks Unit-01, breaking its arm and blasting a hole through its head, with Shinji losing consciousness due to the mental synchronization with the Eva. Just as the situation seems dire, however, Unit-01 goes berserk and fights without any input from a pilot, ravaging the Angel and destroying it.
Shinji recovers after the battle, but the traumatic experience has rattled him greatly. Hoping to help the young boy, Misato decides to take him under her care and assigns him to live with her in her apartment. She also enrolls him in a local junior-high school, where Shinji has trouble assimilating due to one of his classmates, Toji Suzuhara, lashing out at him as a result of his sister being injured in the battle.
Eventually, the Fifth Angel appears, forcing Shinji back into the fray. During the battle, he finds Toji and fellow classmate Kensuke Aida outside the shelter, the two hoping to catch a glimpse of the Eva in action. Shinji brings them both into the cockpit of Unit-01 for protection, then, against Misato's orders, engages the Angel as Unit-01's power supply runs out. With only mere moments to spare before Unit-01 shut down, Shinji succeeded in destroying it. Seeing Shinji so traumatized from fighting the Angels leads to Toji feeling guilty over his previous assault on Shinji, and the two make amends after.
Afterwards, Misato scolds Shinji for disobeying her orders. Shaken by yet another traumatic battle and Misato's harsh words, Shinji wonders about the city and the surrounding countryside for the next few days. He finds Kensuke camping out in a field and spends time with him, only to be found and taken back to NERV HQ by security personnel.
The Sixth Angel emerges and begins to make its way towards the Geofront. Shinji is sortied against the Angel by himself in Unit-01, but the battle immediately goes badly as the Angel fires a powerful particle beam at Unit-01. The Eva is forced back into Nerv HQ, seriously damaged and with Shinji comatose. After Shinji recovers, Rei, who had recovered from her prior injuries, explains that she will fight the Angel in his stead.
Shinji is left despondent over his weakness. Hoping to rekindle his spirit, Misato leads Shinji into the deepest layer of NERV HQ, which holds the body of the Second Angel, Lilith. Misato explains that the Angels are trying to break into NERV HQ to make contact with Lilith, in so doing initiating "Third Impact" and rendering humanity extinct. Now realizing what laid at stake, Shinji agrees to pilot Unit-01 again.
With encouragement from his classmates, Shinji enters Unit-01 to fight the Sixth Angel, with Rei accompanying him in Unit-00. The Sixth Angel possessed defenses that rendered almost every possible attack against it meaningless, so a plan is made to use a prototype weapon, the Positron Rifle, to pierce the Angel's defenses and destroy it. Such a plan calls for the entire power grid of Japan to be channeled into the rifle.
When Shinji fires the first shot, the Angel counters with a massive mountain-melting energy blast. Rei stands in the path of the blast with a shield to protect Shinji, placing her life in jeopardy. Shinji manages to fire off another shot that lands true, piercing the Angel's core and destroying it. With the Angel dead, Shinji rescues Rei from the damaged Unit-00, and the two become close friends.
The war against the Angels is far from over, however...On the surface of the moon, an enigmatic young man named Kaworu Nagisa is contacted by the leader of SEELE, NERV's patron organization, to discuss their next plan. Afterwards, Kaworu looks fondly towards the Earth in anticipation of meeting Shinji...
Back in Japan, Shinji and Gendo both visit the grave of Yui Ikari, Shinji's mother and Gendo's wife. The uncomfortable visit is interrupted by news of the Seventh Angel's appearance. Shinji rides with Misato back towards NERV HQ, only to encounter the Angel. Thankfully, another Eva appears to lay the Angel low: Evangelion Unit-02, piloted by the headstrong German air force captain Asuka Langely Shikinami. She is accompanied by Ryoji Kaji, a fellow NERV agent and Misato's old flame, who comes bearing a present for Gendo: a briefcase containing the "Key of Nebuchadnezzar".
Asuka moves in with Shinji and Misato, complicating Shinji's life as Gendo continues to advance his agenda. Asuka acts very brusquely around Shinji and Rei, but the three bond together when they succeed in fending off the Eighth Angel together. Rei, in particular, develops a desire to help Shinji bond with his father, whom she also shares a close bond with, and makes preparations for the three to have a meal together. Amidst continued international strife and advancing agendas, Asuka learns of Rei's plans and offers to act as the test pilot for the new Evangelion Unit-03 in her stead.
Tragically, the test goes horrifically awry as the Ninth Angel takes over Unit-03, trapping Asuka inside and subjecting her to critical mental contamination as it rampages. Shinji and Rei sortie in Unit-01 and Unit-00 to stop the Angel. With Unit-00 disabled, the Angel attacks Unit-01. Gendo orders Shinji to fight back, but Shinji is unwilling to do anything that can harm or even kill Asuka. Ultimately, Gendo orders the activation of Unit-01's "Dummy Plug", an autopilot system that drives Unit-01 to savagely eviscerate Unit-03 before crushing the Entry Plug in which Asuka is trapped.
Asuka barely survives the ordeal, but is placed into isolation as a result of the contamination she suffered. Meanwhile, Shinji, enraged that his father forced him to nearly kill Asuka, hijacks Unit-01 and threatens to destroy NERV HQ. He is stopped from doing so, but immediately tenders his resignation.
As Shinji boards a train to leave Tokyo-3, however, the Tenth Angel appears and makes its way to the Geofront. As Shinji makes his way to a shelter, Gendo tries to sortie Unit-01 with the Dummy Plug, only for the system to fail to activate.
Mari appears and commandeers Unit-02, disabling the Eva's restraints and savagely attacking the Angel, only to be rebuffed. Rei attempts to destroy the Angel herself with the damaged Unit-00 and a ballistic missile, only for her attack to fail. Worse still, Shinji watches in horror as the Angel devours Unit-00 and Rei, integrating the Eva's biology into itself and breaking through NERV's defenses.
Shinji races back to NERV HQ and climbs into the cockpit of Unit-01, engaging the Angel in a fierce battle, Unit-01 losing an arm in the process. Unfortunately, Unit-01 runs out of power before Shinji can finish off the Angel, and the Angel counters viciously.
As all hope seems lost, Unit-01 suddenly reactivates. Shinji awakens Unit-01’s hidden power and proceeds to ravage the Angel, using its A.T. field to create a new arm and blast the Angel away, before piercing through all of the Angel’s defenses with an eye laser attack similar to the Angel’s. Shinji uses the evolved Unit-01 to pin down the Angel in the hopes of saving Rei. He hears Rei's voice tell him to stop, since she can't leave the core of the Angel, but Shinji persists, diving deeper and deeper into his entry plug, staking his humanity to enter the Angel's core and save Rei. All the while, Unit-01 begins to transcend its physical limitations to grant Shinji's one wish.
Shinji succeeds in pulling Rei out of the Angel, causing the Angel to explode and reform into a giant blood-red Rei that becomes absorbed into Unit-01. As the skies redden and the earth upends itself, Misato recognizes the wings of light jutting from Unit-01's back — the same kinds of wings she saw during Second Impact. Ritsuko confirms that the same thing is happening now: this is Third Impact.
Suddenly, a spear juts down to the earth, piercing through Unit-01 and halting Third Impact. Kaworu descends to the Earth in a new Evangelion, the Mark.06, promising to show Shinji "true happiness"...
Fourteen years have passed since the events of the previous film. Unit-02' and Unit-08, piloted by Asuka Langley Shikinami and Mari Illustrious Makinami, are sent into orbit above Earth to recover a peculiar object: a large Tesseract-shaped sarcophagus, and its contents — Evangelion Unit-01. The Eva units are attacked by a pair of Evangelion Mark.04A EVAs, which Unit-08 and Mari are able to destroy before she's forced to withdraw. Unit-02' and Asuka make contact with the Tesseract, only for one more EVA, a Mark.04B, to appear. Just as it seems the Mark.04 has her dead to rights, Asuka cries out for help from Shinji Ikari...
At that moment, a laser breaches the Tesseract and obliterates the Mark.04, Unit-01 answering Asuka's cries before falling back into hybernation. As the Tesseract and Unit-02 return to Earth, Kaworu watches from below, anticipating his fated meeting with Shinji...
Shinji awakens, finding himself a captive in the hands of the organization known as "WILLE", a group dedicated to the destruction of NERV and the Evangelions. Ritsuko Akagi explains he had been retrieved from the core of Unit-01, along with his SDAT tape player. To his confusion, he receives a cold and distrusting reception from everyone, including Misato Katsuragi, WILLE's leader: the only person who treats Shinji with any kindness is Sakura Suzuhara, his nurse and the younger sister of his friend Toji... who somehow looks old enough to be his big sister...
Unit-01 and the Tesseract containing it is now kept in the core of the Wunder, WILLE's flying flagship. Due to the danger supposedly posed by Shinji in control of an Evangelion, he is forbidden from entering an Eva ever again: to enforce this, he is outfitted with a "DSS Choker", a bomb collar that would detonate and kill him if he ever triggered an Eva's awakening.
The Wunder is then attacked by several Mark.04C EVAs, but with Unit-01 at its disposal, the battleship easily disposes of them.
To Shinji's surprise, Asuka is present. His surprise turns to hurt shock when Asuka, now wearing an eyepatch and having not aged in fourteen years due to the "curse of Eva", bears cold malice towards him.
Confused and dismayed at the harsh treatment he received from his old friends, Shinji suddenly hears Rei's voice calling out to him. Another Evangelion breaches the hull of the Wunder: Evangelion Mark.09, piloted by Rei! Tired of being treated like dirt by the crew of the Wunder, Shinji elects to leave with Rei. Mari tries to stop Rei with Unit-08, shooting off the Mark.09's head to no effect. Before departing, Sakura begs one thing from Shinji: that regardless of what he does from this point forward, he never set foot in an Eva. Ritsuko begs Misato to activate the DSS Choker, but Misato cannot bring herself to do it.
Rei brings Shinji to the ruins of NERV HQ, where he reunites with his father, Gendo, and NERV's vice-commander, Kozo Fuyutsuki. Gendo tells Shinji that he will pilot EVA when the time comes, but tells him nothing else. Shinji is initially elated to be reunited with Rei, only to find that she has no memories of him, and no drive to do anything except follow orders, leaving him confused.
With his SDAT player not working, Shinji finds himself at a loss while Gendo plots and schemes. While walking through the ruins of the Geofront, he meets Kaworu Nagisa, an enigmatic young man who befriends Shinji. Kaworu offers to repair the SDAT player, a memento from Gendo, and invites him to play piano with him. The two bond over their love of piano, with Gendo and Fuyutsuki observing Shinji's interactions with "SEELE's boy". In time, Kaworu reveals the truth of the strange world Shinji awakened in to him; fourteen years had passed since "Near Third Impact", a cataclysmic event that Shinji inadvertently caused, resulting in the Earth being coated in toxic blood-red liquid that rendered the near-entirety of the Earth uninhabitable. Furthermore, NERV's plan was to intentionally start Third Impact, as part of their "Human Instrumentality Project" — the decimation of the human race to merge of all the souls of humanity into a singular entity. Shinji is shocked at the devastation he caused, all because he wanted to save Rei. Kaworu explains that humanity doesn't see it that way, thus explaining WILLE's hostility towards him.
Fuyutsuki invites Shinji to play a game of shogi with him. During the game, Fuyutsuki reveals further truths about his mother: first, that Yui Ikari's maiden name was "Ayanami". Yui, who bore an uncanny resemblance to Rei, was thought dead following the first contact tests of Evangelion Unit-01. In truth, however, Yui still lived inside Unit-01's core as its control system. Following Yui's disappearance into Unit-01, Gendo attempted to clone Yui, creating a long series of clones — all named Rei. The realizations are devastating: Shinji never saved Rei from the core of an Angel fourteen years ago, so he had nearly exterminated mankind for nothing. Shinji tosses his father's SDAT player aside in lament, until Kaworu tells him that there is a chance he could make things right, a way to reverse the effects of Near Third Impact. All they had to do was climb into the controls of NERV's latest Eva unit, Evangelion Unit-13, and extract the Lance of Longinus and the Spear of Cassius from the depths of Terminal Dogma. To demonstrate his willingness to help Shinji, Kaworu takes the DSS Choker off of him and places it on his own neck, explaining that it was actually meant for him.
By Gendo's orders, Shinji and Kaworu enter Evangelion Unit-13 and descend into Terminal Dogma. On the way, Shinji comments that the Rei accompanying them is not the "real" Rei, causing Rei to suffer an identity crisis. In Terminal Dogma, they find Lilith's rotting corpse, merged with the Evangelion Mark.06, impaled by two spears. Kaworu notices something off, however: the two are both Lances of Longinus, with no Spear of Cassius.
Detecting Unit-13's activation, Misato sends Asuka and Mari after it with Unit-02' and Unit-08. Rei joins the fray in the Mark.09 to fend off Mari and Asuka, who is determined to stop Shinji, even if it means killing him. Unit-13, however, eventually prevails after Unit-02's battery runs out.
Asuka and Kaworu beg Shinji to stop, but Shinji is dead-set on making things right, ignoring their pleas as he extracts both Lances from Lilith's corpse. Following her orders, Rei decapitates the now-freed Mark.06, releasing the Twelfth Angel that it was containing. Unit-13 consumes the Angel, and begins to transcend in a similar manner to Unit-01 fourteen years ago: this is the beginning of Fourth Impact!
The Wunder appears and attempts to stop Unit-13 before suddenly being disabled by the Mark.09, which is now operating automatically due to a SEELE program. Growing a new head, it then lands on the battleship and hijacks it; the EVA was originally designed to control said battleship. Asuka activates Unit-02's Code 777 Beast Mode in order to fight it. Rei, sitting helpless in the Mark.09, asks Asuka what Rei Ayanami would do, to which Asuka answers that she doesn't know, instead asking Rei what she would. Rei chooses to eject from the Mark.09, giving Asuka an opening to destroy the Mark.09. However, the Mark.09 turns out to be stronger than expected, and Asuka is ultimately forced to trigger Unit-02's self-destruct mechanism before ejecting, which successfully destroys the Mark.09.
As the Earth is upended beneath Unit-13, Kaworu reveals to Shinji that he was actually the First Angel, but had cast himself down to the Thirteenth Angel in an attempt to stop Fourth Impact. Upon sensing his Angelic nature, the DSS Choker activates and prepares to kill Kaworu. Kaworu says his farewells to Shinji, smiling warmly at him as Shinji is unable to do anything but watch as Kaworu dies.
Kaworu's death, however, doesn't stop Fourth Impact. It is only through Mari extracting Shinji's Entry Plug from Unit-13, realizing he was still being used by SEELE, that the disaster is thwarted.
Afterwards, Asuka opens Shinji's Entry Plug to find him catatonic. Though she still bears a great deal of malice towards him, she forces him to his feet and, along with Rei, make their way to meet up with the other "Lilin"...
In the ruins of Paris, a team from WILLE, led by Maya Ibuki, are working on some kind of device called the Anti-L System. They are soon attacked by NERV forces, who are quickly repelled by Mari Makinami Illustrious in the partially-repaired Unit-08. The WILLE team finishes their work, and the Anti-L System restores Paris to its original state, allowing them to scavenge parts to repair the EVA units.
Meanwhile, Asuka Shikinami Langley, Rei Ayanami and the still despondent Shinji Ikari are wandering through the ruins of Tokyo-3. They eventually find a settlement of survivors of the Near Third Impact. Among the inhabitants are Toji Suzuhara, Hikari Horaki and Kensuke Aida, now adults. Toji is the settlement's doctor and has a child with Hikari, while Kensuke is a technician. All of them are happy to see Shinji alive, but Shinji doesn't respond to them.
Over the following days, Rei explores the village, helping the women farm and take care of domestic tasks, and learning about human interaction and society. Shinji, however, remains catatonic, neither eating nor responding to any interaction. The only thing he responds to is the sight of Asuka’s DSS Choker, which causes him to panic and vomit. Asuka, who is living under the care of Kensuke, becomes frustrated with his unresponsiveness and force-feeds him to keep him alive. This only makes Shinji relocate to the lake where NERV Headquarters used to be, in the ruins of the Eva-01 hangar, where his catatonia continues. Eventually, after Rei is persistent in attempting to reach out to Shinji with her newfound kindness, he cracks and returns to the village.
Kensuke takes Shinji with him on his daily tasks, explaining that WILLE is helping the village survive, and provided the Anti-L system we saw at the start of the movie, which protects them from the effects of Near Third Impact. He later introduces Shinji to Ryoji Kaji, the son of Misato Katsuragi and the late Ryoji Kaji.
Rei’s health suddenly deteriorates, and she realizes that she can’t survive beyond the reach of NERV. Speaking to Shinji for the final time, she gives him back his father's tape player and expresses sadness at not being able to experience life, but is happy nonetheless for her short experience with it, before decomposing into LCL.
The Wunder arrives to pick up Asuka. Shinji, having fully recovered, decides to go with her. Onboard the Wunder, Misato talks to Ritsuko Akagi about the elder Kaji; upon realizing that the Human Instrumentality Project would wipe out life as everyone knew, Kaji sacrificed himself to stop Third Impact. It was he who had seized the Wunder from NERV, planning on using it to preserve as many lives as he could: deep inside the Wunder are enormous seed vaults, which humanity could someday use to rebuild. Misato plans instead to use the Wunder to destroy NERV and stop the Human Instrumentality Project once and for all.
Gendo Ikari and Kozo Fuyutsuki have moved base to Antarctica (the epicenter of Second Impact) and are preparing to restart EVA Unit-13. Gendo reveals that he let the Rei clone die in order to make Shinji feel the same loss he had felt when losing Yui.
Wunder prepares to attack Antarctica. It deploys its seed vaults into geostationary orbit, awaiting the day humankind can retrieve them. Before the mission, Asuka admits to Shinji she once had feelings for him.
Upon arrival, Wunder is attacked by a NERV battleship commanded by Fuyutsuki. Though WILLE is unable to damage it, they manage to break through. Another NERV battleship attacks, but the Wunder perseveres and arrives at NERV Headquarters. Asuka and Mari sortie in their now-repaired EVAs to disable Unit-13 before it can reactivate. Fighting their way through a swarm of NERV EVAs, Asuka and Unit-02 make it to Unit-13, but Unit-02 refuses to attack, blocking itself with its own AT field: it’s afraid of Unit-13. As a last resort, Asuka removes her eyepatch, unsealing the Ninth Angel contained within, converting herself and Unit-02 into an Angel so she can make the attack herself. However, Gendo had been waiting for this to happen: Unit-13 suddenly activates and absorbs Unit-02. Moments before being absorbed, Asuka is approached by her "original", revealing her to be a clone from the Shikinami series. Her DSS choker activates too late to stop her from dissolving into LCL.
In the meantime, the Wunder is attacked and disabled by a third NERV battleship, then hijacked by a new EVA, Mark.09-A. It is revealed the Wunder was once one of the same NERV battleships, before Kaji stole it while it was still under construction. The Wunder’s presence was itself part of Gendo’s plan: the four ships were designed to substitute for the four Adams that started Second Impact, and with all four back together, Gendo is able to begin another impact event.
Misato and Ritsuko confront Gendo. Ritsuko shoots him to no effect, revealing Gendo has used the Key of Nebuchadnezzar to transcend humanity. Gendo reveals that the purpose of the Shikinami and Ayanami clones is to enact the Human Instrumentality Project. He leaves in Unit-13 after retaking Unit-01.
A determined Shinji asks Misato to let him pilot Unit-01. Sakura Suzahara and Midori Kitakami, still bitter over Shinji's triggering of Near Third Impact and destroying their families, try to stop him, but Misato protects him, taking a bullet from Sakura in the process. Misato apologizes to Shinji, saying that she was wrong for blaming him and will take responsibility for his actions. Sakura and Midori are still angry, but ultimately decide to let it go. Mari has Unit-08 consume the Mark.09-A, freeing the Wunder from its control, before taking Shinji to the anti-universe created by the new impact event, where Unit-13 and Unit-01 are currently located.
Entering Unit-01, Shinji finds a specter of the original Rei Ayanami from the first two films at the controls. She apologizes for not being able to spare him from having to pilot an EVA, but Shinji assures her it is alright.
Now in control of Unit-01, Shinji steals one of Unit-13's Spears of Longinus, transforming it into the Spear of Cassius. Whereas Longinus is the spear of despair, Cassius represents hope. Gendo shows Shinji the "Golgotha Object", an object left by an unknown precursor that can bend fate.
Gendo and Shinji then fight within the anti-universe, which takes the form of various locations from Shinji's memory. They are perfectly matched, with neither able to gain an advantage over the other. Realizing it is useless to fight, the two must connect emotionally in order to resolve their long conflict. Gendo shows Shinji “Eva Imaginary”, an Evangelion in the form of a black Lilith, which can only exist in the Anti-Universe where reality and fiction are the same. Gendo impales it using the Spears of Longinus and Cassius, transforming Eva Imaginary into a Giant Naked Rei, the culmination of the Human Instrumentality Project, which commences as it emerges into the regular universe.
Mari confronts Fuyutsuki. She refers to him as "sensei", while he calls her "Mari Iscariot", suggesting they have both known each other for a long time. Mari deduces that Fuyutsuki’s goals don’t entirely align with Gendo’s, and Fututsuki agrees, stating that he’s ensured Mari will have what she needs for what she’s going to do next. Fuyutsuki is then reduced to LCL by the ongoing impact. Mari then uses Unit-08 to consume the EVAs controlling the three NERV battleships — as Fuyutsuki made possible — which also destroys the battleships themselves.
Shinji approaches his father, but an AT field springs up between them. To Gendo’s surprise, it’s his own: he’s afraid of his son. However, Shinji only intends to return his father's tape recorder, which passes through the field easily, and we finally learn its significance: Gendo had used the headphones to isolate himself from others in his youth. He had hated social interaction and connecting with others, though he was never actually lonely, since he had been alone since childhood. One day, however, Mari (now revealed to be a contemporary of Gendo) introduced him to Yui Ayanami. Through Yui, Gendo found that being with others could be enjoyable, and they eventually fell in love. Her apparent death traumatized him, as for the first time, he experienced true loneliness. Thus, his plan is to initiate the Additional Impact to reunite with her. However, as he searches his memories for Yui with increasing desperation, he only sees Rei in her place.
Misato, having evacuated the crew of the Wunder, crashes it into the Giant Naked Rei, sacrificing herself and destroying the ship to create a new spear, "Gaius", the spear of will, which has the power to rewrite the world. This spear passes into the Anti-Universe, appearing in Shinji’s hands.
Gendo now realizes he still had Yui all along in his son, and apologizes to Shinji for pushing him away. He takes his leave of Shinji and disappears.
With his father having found closure, Shinji turns to Asuka. As the only successful clone in the Shikinami series, she had also grown up alone, and put all her effort into becoming a top EVA pilot, so that she wouldn't need anyone. But in the end, she was still lonely. Kensuke appears and reassures her everything is okay. Shinji and Asuka both appear on a beach, where Shinji thanks her for saying she liked him, and admits he liked her, too, before she is ejected from Unit-13.
Shinji then speaks to Kaworu (whose soul is still inside Unit-13), realizing now that both of them have met many times already, their names being next to each other in the "Book of Life"; the two of them experiencing the events of Evangelion over and over again. Kaworu admits that he piloted EVA to try and find happiness for Shinji, in the belief that he would find his own happiness as well. The elder Kaji then appears, telling Kaworu that his own happiness should not be tied to Shinji's. Having now found his closure, Kaworu departs with Kaji.
All that remains now is Rei. Rei says she is happy as she is, but Shinji tells her the "other" Rei was able to find a place to belong without an EVA; she will too. He has decided to use Gaius to rewrite the world into one without EVAs or Angels, a "Neon Genesis".
Shinji prepares to sacrifice himself with the Spear of Gaius. However, Yui suddenly appears and pushes him away. Together with Unit-01 and Unit-13, Gendo and Yui sacrifice themselves in Shinji’s place, wiping the EVAs from existence and stopping Fourth Impact. The Giant Naked Rei disintegrates, and every human and animal transformed by the Near Third Impact is restored and slowly descends to Earth.
Shinji sits contentedly on a beach. The art gradually degrades from animation to keyframes to motionless sketches, until Mari suddenly arrives before Unit-08 (and the EVAs it consumed) also disappears, and tells him to come with her.
In the final scene, an adult Shinji is in a train station in a new reality that resembles present-day Japan, along with adult versions of Rei, Kaworu, Asuka, and Mari. Shinji leaves the station with Mari. The movie ends with a long pan of the new, real world, untouched by any Impact.
