Disclaimer: I will be explaining the whole series, so there will be spoilers.
Perhaps one of the most misunderstood series, Neon Genesis Evangelion has been the subject for many liberal and imaginative interpretations. In addition, due to the public's general confusion and outrage at the latter episodes, the creator has been forced to rewrite the series with subsequent movies. This is my third time watching the series. Either I got smarter or more mature (or more crazy), but everything made sense this time around. Ironic, that an animated series targeting teenagers makes more sense for a 30+ year old.
With my first exposure, back in 1998, as a 5th grader (the series aired from 1995 to 1996), I was drawn in by the visceral elements of the series, though I only watched the first few episodes. With my first time watching the whole series in the early 2000s, as a high schooler, I was entirely in the confused and frustrated crowd. However, with my most recent rewatch, I found the entire series to be surprisingly coherent, and with surprisingly few plot holes or loose ends. After about 20 years, I am finally able to make sense of the whole thing, and I really want to explain it here, to simply convey the true story that has been buried in the series for all these years. The 26 episodes are conclusive and consistent. There's really no need for more.
The series begins in the year 2015, 15 years after the "Second Impact", where Shinji Ikari, the son of Gendo and Yui Ikari, is summoned by his father to command the Eva Unit 01, what seems to be a gigantic robot, against alien beings attacking the Earth, which have been labelled as "Angels". In his first battle, Shinji is hesitant, unconfident, and bitter about only being called upon by his father whom he has not had contact with for 15 years, only when his father needed him for something. Ultimately, he begrudgingly accepts, only to be defeated by the Angel. The Angel deals a blow to the Eva's head, which is mentally connected to Shinji. Bafflingly, the Eva then restarts independently and aggressively defeats the Angel. Eva Unit 01's helmet falls, and Shinji, and the audience, is given a glimpse of Eva Unit 01, something alive which terrifies him.
The next 12 episodes are fairly linear and characteristic of Shonen anime, where basically the good guys win against further Angel attacks. Battles take place on land, in the air and sea, in outer space, in a volcano, and even in the supercomputer, Magi. Rei Ayanami, the pilot of Eva Unit 00, and Souryu Asuka Langley, the pilot of Eva Unit 02 make their entrance. It is notable, though, that with each battle, the city, new Tokyo-3 sustains more damage, and the Angels get closer to the command station: Central Dogma. However, up to this point, the net result has been positive, and the damage is smoothed over by the good news. Even though the city is damaged, the team becomes more cohesive mentally.
Perhaps signaling a turning point, episode 14 recaps all the episodes up until then. The next 10 episodes then follow a new trend, where the net result is negative, as fatigue begins to take a toll on the entire team. The cracks begin to show as the team gradually breaks down. These episodes become more psychological, as towards the end, even the Angels are attacking the pilots psychologically.
In a mundane scene in episode 15, Gendo Ikari gives a few thoughts, which become vital to understanding the entire series later. As he is visiting the grave of his wife, Yui, Shinji's mother, he tells Shinji that the grave is ornamental, there's no body, that everything about Yui is in his heart, and that that's enough for now.
Shinji's friend, Touji, is selected as the fourth pilot, to pilot Eva Unit 03. However, Eva Unit 03 becomes infested with an Angel, and Shinji is ordered to defeat it. Refusing to do so, Shinji is disconnected from Eva Unit 01, and the dummy plug is used to control Eva Unit 01, instead. He watches helplessly, as Eva Unit 01 brutally destroys Eva Unit 03, stopping only after crushing the entry plug housing the pilot. This event causes Shinji to hate piloting the Eva Unit 01, and to refuse to do so, only to later return when he recognizes that it is something he must do.
More of the NERV organization is gradually revealed to the audience. 2008 feet below Central Dogma is Terminal Dogma, where the first Angel, labelled Adam, is being held, who was purportedly, the cause of the "Second Impact", an event that occurred in the year 2000, in Antarctica, causing the snow cap to melt. This stated cause becomes questionable as Gendo Ikari behaves in a manner that would be inconsistent if a "Third Impact" were imminent.
It is also revealed that Rei Ayanami was created shortly after Gendo's wife Yui vanishes. She resembles Yui, and has the name that Gendo would give his offspring if she were a daughter. Rei has clones, and is part of the Dummy plug project, a project to automate all the Eva units using Rei.
Eva Unit 01 goes berserk again, shedding its armor, revealing that the Eva units are actually alive, and mysteriously linked to the Angels.
Asuka is surpassed by Shinji, and gradually breaks down, as she enters a positive feedback loop, where her deteriorating mental condition causes her to be unable to control Eva Unit 02. Ultimately, she is psychologically attacked by an Angel, but refuses to back down, knowing that her defeat will mean her being dismissed from being an Eva pilot. This refusal subjects her to mental anguish, and she becomes a despondent shell of her former self.
Kaoru Nagisa, the fifth pilot emerges. He is able to synchronize with all the Eva units with ease. Turns out, he is the last and final Angel. Seeking to reunite with Adam, he breaks into Terminal Dogma, only to realize that "Adam" was actually "Lilith". Shinji is sent to destroy him, and does so after some deliberation, having bonded with him in their brief time together.
Finally, the Human Complement Project is completed - a project where all human minds are joined together. Critically, everyone's impression of everyone else is also united. This was the goal of Gendo Ikari, ever since his wife disappeared, as this was the closest he could get to bringing her back - by gathering everyone's impression of her together. The last two episodes revolve around this, and is basically when all the characters do some soul-searching. Initially, all the main characters are explored, but the scope quickly narrows down to Shinji in the final episode, as by then, there wouldn't be enough time to thoroughly explore all the characters.
Shinji ultimately realizes that it was only his subjective view of the world around him that was making life difficult, and that as he accepted himself, life wouldn't be so bad. While this epiphany would be great in the real world, with the Human Complement Project, it seems that everyone is isolated in a world of their own creation. And with him being instantly surrounded by an applauding audience, it feels of self-delusion.
Perhaps just as important as the plot are all the characters in the series. Many episodes focus on individual characters. Many of the characters develop throughout the series. Even side characters reveal their perspectives in some of the later episodes. Here, I'll go through some of them.
Shinji Ikari is the "Third Child", or the third person identified to be a Eva pilot. He is the son of Gendo and Yui Ikari. With limited interaction with his father, he is timid, sensitive, and afraid of people. He grows and develops throughout the series, which more or less revolves around him. The closest to a romantic attachment he has is with Rei Ayanami, the "First Child", who resembles his mother, even though he doesn't actually remember his mother clearly.
Misato Katsuragi is a Colonel, who calls the shots in most of the Angel attacks. She volunteers to be Shinji's caretaker, and fulfills that role sufficiently, giving Shinji encouragement when he is weak. While she is pragmatic on the job, she does have an emotional side. She was intimately involved with NERV from the beginning, as her father was a researcher, and she was the sole survivor of the "Second Impact". She has a long history with Kaji and Ritsuko Akagi, who are both around the same age as herself. Kaji is the man she fell in love with 8 years ago, but whom she left as she discovered how similar he was to her father, whom she hated. Despite that, she still had feelings for him, and was devastated when she mistakenly killed him. Despite being high up on the chain of command, she was ignorant of NERV's secrets, but began to have reservations after Kaji showed the first Angel, hidden in Terminal Dogma, to her.
Ritsuko Akagi is the lead researcher, who is responsible for most of the experiments. She is the daughter of Naoko Akagi, who developed Magi, the supercomputer that NERV relies on. She is more pragmatic than Misato, never talking about her personal life, and rarely showing emotion. She was part of the "in" crowd, having knowledge of all the NERV secrets, including Adam and the Dummy plug project. She also romantically loves Gendo Ikari, but her love goes unrequited. Being provoked by the death of her cat, and by her being seemingly sacrificed to shield Rei, her jealousy drives her to destroy Rei's clones.
Kaji is the third in the group. He is both a NERV employee as well as an Interior Affairs department operative. His loyalty is to himself, as he tries to discover the truth, which ultimately costs him his life. He is unscrupulous, but shows discernment and restraint at crucial moments. Perhaps most baffling is that when faced with death, he chooses to be watering his plants, rather than to be in the embrace of his lover.
Rei Ayanami is the "First Child". She was the original Eva pilot, and pilots the prototype Eva Unit 00. As she was created, and has clones, she feels that her life is unimportant, and readily sacrifices it for people she cares about, most deeply of whom is Gendo Ikari, followed by Shinji. She obediently sustains injuries at Gendo's command, but Gendo does protect her whenever possible. She shares a special bond with Gendo, despite being emotionless, in general. She also develops as the series progresses, becoming slightly more emotional and human.
Asuka Langley is the "Second Child". She is fiercely competitive, but is very insecure inside. Lacking parental love and care, she resolved to be self-reliant from an early age. Nevertheless, she desires affirmation from others, and her unceasing comparisons to others' treatment of herself leads her to become initially frustrated, and ultimately resigned. She is romantically attracted to Kaji, but he brushes off her advances.
Gendo Ikari is the Commander of NERV. He is a mystery, as he seldom talks, and people generally don't know about his past or his personal life. He married Yui, who was a bioscientist, working for NERV. While he was always reserved, he seemed to soften up during this time. After his wife's disappearance, he changed, and dedicated his all to the Human Complement project. His one and only love was probably his wife, as he did not reciprocate the affections of the Akagis. Whether due to his personality, or out of necessity, he unwaveringly makes decisions that sacrifice sympathy and emotion for progress and survival. In the end, it seems that he accomplished his goal, as he is seen with his wife in the final scene.