A teenager named Shinji Ikari goes to Tokyo-3 city due to a request from his father, Gendo Ikari. While meeting with Misato Katsuragi, an employer from Gendo, the city is attacked by a giant created known as Angel, that confronts the army. Misato takes Shinji to NERV, an organization headed by Gendo that developed giant bio-mechanical mecha known as Evangelions. As the Evangelion Unit-01's pilot, Rei Ayanami, is injured, Gendo asks his son to pilot Unit-01 to defeat the attacking Angel. Shinji decides to fight the Angel, but he panics when seeing the Angel. Before being killed by the Angel, Shinji makes Unit-01 furiously attack the Angel, which self-destructs, causing minor damage to the Evangelion. Next day, while Shinji is recovering in the hospital, Misato discovers that Gendo is not planning to live with him. As such, Misato decides to be Shinji's legal guardian, to avoid him being alone.
Stage 01: Angel Attack
The manga starts with a monologue by Shinji, describing his mental state:
I've never had any cherished ambitions. I don't aspire to any future profession or career. So far, in the first fourteen years of my life, things have always happened as they had to. And things will probably continue the same way. That's why I've never really cared whether I got into an accident or something and died.
I wrote that in an essay for school, and predictably, the teacher yelled at me... and asked to take the assignment seriously.
A mysterious creature appears silently underwater, and armies of the UN are ready for battle, and suddenly a big splash comes from the water. The next page switches to NERV's Command Center, and we see Gendo with Fuyutsuki and Gendo confirms that, with no mistake, the being is an Angel.
An alarm declared in the city of Tokyo-3, and being attacked by a monster. In the train station, Shinji tries to call Misato Katsuragi but can't due to the lines being off. Soon afterwards, Shinji notices a flying fighter and cruise missiles inside the city, fighting the monster. The missiles hit the monster to no effect, and it counters with lance of light from its hand, destroying the VTOL. Misato comes to Shinji and he gets in the car, Misato tells Shinji that being is called an Angel, and the conventional weapons have no effect on it. The Angel tries to attack them, only to see an "Evangelion" rushing at it, knocking the Angel and helping them, while they try to go away, the Angel knocks the robot down. The UN prepares for N² mine on the Angel, blowing the whole city with only minor damage to the Angel. The mission of destroying the Angel, is given to NERV. Misato and Shinji finally reach GeoFront, and she welcomes him in it. Shinji wonders why his father summoned him. Gendo orders to "re-initialize" Unit-01, and says that the spare pilot has arrived.
Stage 02: Reunion
This stage starts with the arrival of Shinji and Misato to NERV Headquarters, and Misato is lost inside, Ritsuko comes from the elevator. Ritsuko notices Shinji and introduces herself to him. Meanwhile, Sachiel has recovered from the N² mine explosion and continues its advance towards Tokyo-3. Gendo orders Battle Stations Level One, and leaves the command to Fuyutsuki. before Shinji, Misato and Ritsuko arrive at the location Ritsuko wanted to show to Shinji. Ritsuko tells Misato that the Angel may have an A.T. Field, and it has an artificial intelligence capacity, just like the Evangelion. They reached their destination, the place is so dark, Ritsuko turned the light, revealing the "Evangelion" that Shinji has seen before. Ritsuko tells Shinji that the Evangelion not a robot, but a giant Artificial Human (cyborg). Shinji wonders if that is what his father works on, and Gendo appears to him, and orders him to enter the Evangelion and fight the Angel. Misato objected Gendo, saying that it took Rei seven months to synchronize with her Evangelion, and Shinji just arrived today. Ritsuko tells Misato that their high priority is to repel the Angels. Shinji rejects at first, and Gendo calls him a coward, and orders Fuyutsuki to wake Rei. Rei arrives at the hangar, who is badly injured, is ordered to pilot Evangelion Unit-01 again. Finally, Sachiel discovered the location of the GeoFront.
Stage 03: Unit-01, Lift Off
Sachiel has found the location of NERV Headquarters and began setting explosions over the city. Shinji wonders why would Rei want to pilot the Evangelion with such injuries, and Misato motives him to pilot. The preparations of Evangelion Unit-01 for launch start finally, and ready for launch. Evangelion Unit-01 is launched with Shinji for his first time, and once the Evangelion reached the surface, Shinji has faced the Angel itself. Misato wishes Shinji good luck.
Stage 04: Silence...
Evangelion Unit-01 has reached the surface, and is facing the Angel. Shinji tries to walk and then to stop, but the Eva didn't stop, thus orders it to charge. Shinji missed the Angel and collides with a building and falls. Shinji is frightened and can't move, and the Angel grabs the Evangelion from the head, and break its arm and resumes by stabbing its head. The head is heavily damaged and Evangelion has gone completely silent, and all the connections with the Eva are lost.
Stage 05: Angel Fire
Shinji has gone unconscious and in his psyche thinks he is dead, but a light comes to him. He thinks that it's his mother, but is revealed to be the Evangelion itself, and refuses to die, therefore the Eva has gone "Berserk". The Eva has gone out of control, and charges at the Angel, kicking its head and avoiding the Angel's attack. Misato is surprised with the Eva's movements and thinks that it's Shinji's doings, and Ritsuko denies that he can't be at that level yet. The Eva charges again but stopped by the Angel's A.T. Field. The Eva regenerates its broken arm, and deploys an A.T. Field as well, and breaks through the A.T. Field. The Angel fires at the Eva but its beam has been reflected and the Angel falls. The Eva attacks the Angel's Core with its knees, and starts breaking it. The Angel wraps itself on it, and self-destructs. The Angel has exploded but the Eva just sustained minor damage. Shinji's life signal has been confirmed.
Stage 06: I... Cry...
Shinji is running in a dark street, and suddenly sees the Evangelion's Angelic part, and scream. He wakes up in the hospital, and realizes that it was all a dream. Meanwhile, Gendo is now with the Human Instrumentality Committee, discussing the budget on repairing both Unit-00 and Unit-01. They also remind him of their ultimate goal, The Human Instrumentality Project. In the hospital, Shinji is wandering if all of what he did was just a dream as well, but sees the injured Rei, and Gendo comes to visit her, and just looks at Shinji. Misato comes to pick Shinji up and asks him if it's alright to live alone, and he replies that it's ok and none of her business. That angers her, and she calls Ritsuko to tell her that Shinji will be living with her. Misato takes Shinji to see the city of New Tokyo-3. Misato tells Shinji that it's the city he defended, and Shinji cries saying that he wanted to hear her praise words from his father.
- Even though it's the start of the manga, it also differs from the TV series. i.e.:
- Shinji is living with his uncle after Gendo abandons him, not with his teacher.
- Rei pilots Unit-01 to fight Sachiel, but she hasn't piloted it in the TV series.
- For some reason, the fifth chapter "Angel Fire" was also known as "What was seen in the well of light".
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