Three months prior to the television release of Neon Genesis Evangelion, Anno Hideaki wrote an article for Anime FX, a popular Japanese-based magazine, speaking out against suicide. Within the article, Anno also offers something of an explanation to what many perceive as a very dark and lonely tale:

I started the story with a setting from which I had purged all feelings of optimism. (Anno)

This may appear to be proof that Evangelion is simply a dreary and entirely too-pessimistic creation, but this is the starting point from which Anno had to launch Eva. The director had spent most of the years after his great success, Nadia: Secret of Blue Water, a popular anime, in what he perceived to be a very great depression. As he realized that this onus was hanging over his head, he resolved to act:

I began this thinking just one thing: "I mustn't run away" -- after having done just that, run away, for four years -- where all I was doing was simply not dying. (Anno)

His obligation, as he perceived it, was to face his fear by creating two characters, both weak and flawed, who would face their own inadequacies and problems and stand up to them.

Perhaps the first character of the two that he would create expressly to represent himself is Katsuragi Misato. Misato is an extremely lonely character, for she is without family or friends. Her father, whom her feelings for even she cannot fathom, was killed in the "Second Impact," an event to which she is the sole witness, leaving her catatonic for five years. When she surfaces, she is a seemingly boisterous character whose "noise" barely covers her feelings of depression and inadequacy. She takes up with men only to find that those she falls hardest for are most like her father. Fearing this, she flees them, punishing herself while falling ever farther into herself. Anno tells us that "she protects herself by running away into relationships that are strictly on the surface," but we can see that even this causes her pain (Anno). She is a tragic figure, for she perceives her errors and begins to change almost too late, as she comes to full acceptance of her flaws only in the last moments of her life.

The primary antihero Anno created is Ikari Shinji, who stands in for Anno. Shinji is a fourteen-year-old boy, whose father deserted him at the time of his mother's death. The father, Ikari Gendou, purged all possessions related to Yui, his wife, and this included Ikari Shinji. The child grows up from the age of five with his uncle and sensei. As Shinji's creator describes:

Convinced that, since he feels abandoned by his father, he is an unwanted person, he is yet a coward, unable even to commit suicide. (Anno)

This is the same manner in which Anno describes himself: He exists, where the only item that is accomplished is avoidance of death. About both characters, Ikari Shinji and Katsuragi Misato, Anno tells us:

They are both afraid of being hurt. (Anno)

Within Eva, various characters mirror Anno's words when discussing Shinji. This reinforces the feeling that the director forced himself to completely discover and recreate the events of his life in depression and fear. Though Anno calls the work "perhaps derivative," it is an excellent dissertation on what it is to be alone.

Inside the tale, Misato is an agent of Nerv, an agency under the U.N. that is responsible for the Evangelion Units and therefore, humanity's defense. As such, when Shinji comes to Nerv to become the pilot of Eva Unit 01, she offers to become his foster parent, or at least allows him to live with her. She is given this opportunity because Ikari Gendou, the commander of Nerv, has absolutely no desire in Shinji as a person; he has only the need for an effective pilot. In the third episode, entitled "Unringing Telephone," itself a description of loneliness, Misato discusses Shinji's inability to interact with people with Akagi Ritsuko, a scientist within Nerv. Ritsuko explains the "hedgehog dilemma," that which she believes to be Shinji's difficulty:

If a hedgehog wants to give his warmth to other hedgehogs, the closer he approaches, the more they injure each other. It's the same with some people. Because he is frightened by the aches in his heart, he now seems so cowardly. (episode 3)

Ritsuko's words embody Anno's beliefs. She calls the boy a coward who believes that he is saving others pain by containing his own within himself. Shinji fears the heartache of being deserted and unwanted by his father, so he restrains himself. Misato answers Ritsuko:

He will realize in time that in growing up, people learn to get a sense of distance for each other's hurt feelings. (episode 3)

Misato speaks out of her own torment here. She believes that it is such with all people because this is her experience, the source of her pain. Misato reveals her own weaknesses, believing them to be universal truths.

Despite the inherent weaknesses and pain within these two, by the third episode, we begin to see that they may yet change; that the fog may be lifted from before their eyes. While Shinji is battling the second Angel, his movements are hampered by two of his classmates, Suzuhara Toji and Aida Kensuke. Misato sees that he feels unable to fight because they may be harmed, and she orders Shinji to take the boys into Evangelion Unit 01 with him. Due to the precious moments that he has lost, the Angel gains the upper hand by slicing the energy cable that powers the unit. With only five minutes of precious backup energy remaining, Misato orders Shinji to withdraw. Shinji does not comply, replying simply at first, and then with berserk fanaticism:

Don't run away, don't run away, don't run away! (episode 3)

Shinji's rage is loosed upon the Angel, and even as the Evangelion is drained of its last rations of power, Shinji defeats the enemy. All is not well, however. Immediately upon defeating the antagonist, the young man plunges into despair and racking sobs.

Episode four, named both "Hedgehog's Dilemma" and "Rain, After Running Away," already shows us that Shinji is far from healed. Frightened by what he has done, he leaves Misato and travels around Tokyo-3 by train, considering what he has done. Shinji might not be on the road to recovery yet, but he has revealed his knowledge of Anno's powerful mantra, for within Evangelion, it becomes Shinji's "Don't run away."

The young pilot finds that not running away is insufficient; he must also seek out the cause of his torment. He begins with small steps, asking his fellow pilots why they get into Evangelion. For Ayanami Rei, it is her link to "all people," and for Soryu Asuka Langley, it is to be the proof of her existence. For Shinji, neither of these reasons is correct. In the twelfth episode, "The Worth of a Miracle," Shinji returns to his chant prior to battle, as images of his painful childhood and his father flash through his head. Unlike his uncontrolled first encounter with this decision, he instead uses the mantra to calm his fear and strengthen his resolve, whispering "Don't run away." This time against the Angels, Shinji is the true hero, and his father finally praises him for it:

I've heard the story. You did it, Shinji. (episode 12)

At this slight approval he is awed, and he believes that he has found his raison d'être:

When I heard my father's words, I found that for the first time, I was glad to be praised. And I also found that... that I pilot Eva just to hear my father say those words. (episode 12)

It is not this. This is what he wants to believe, but it is not so. It would be too easy, and the last person whom he would expect, himself, confronts him with this fact. Swallowed within a strange, void-like Angel, Shinji is subjected to a test of the limits of his endurance by surviving on reduced life support within the Eva. Pushed to the brink, he escapes into a hallucination where he speaks with another version of himself. The pilot Shinji is represented as a vertical bar of static, while his conscience is represented as a horizontal one within the anime, as it is here:

|: Father called me by name. I was praised by my father. -: You'll live by simply recalling those pleasures? |: If I trust their words, I can just keep living from now on... -: ...by deceiving yourself? |: Everyone does it. People live by doing so. -: If you continue to think that you can't change yourself, you cannot live on... You have been closing your eyes and turning deaf ears to anything that you did not want to know... You can't live by spinning only a thread of happiness. Particularly, I can't. (episode 16)

This forces Shinji to come to terms with the fact that he has a responsibility to grow as a person. His conscience is dying on the vine, and so he must choose to live for himself and not for others.

Old habits die hard, as they say, and Shinji does not take immediate action. This time, it is Rei who forces him to view his own actions, telling him that he is, "...running away from disagreeable things" (episode 19). This time, for the first time, Ikari Shinji steps into Evangelion of his own accord. He faces the most powerful of the Angels thus far, as it has already defeated the other pilots. Shinji is the last bastion of defense, and he knows it. The pained young man is quickly beaten back by the Angel, and with no power reserves and the Angel merely toying with his limp and almost lifeless body, he crosses a line:

...Move, move, move, move, please move! If you don't move now, if I don't do it now, everyone's going to die! I couldn't stand that anymore. So please move! (episode 19)

For the second time in the series, Shinji's Eva moves under no other power than his own force of will. Bestial in its aggression, voracious in its destruction, the juggernaut that the Evangelion has become as an answer to Shinji's prayers/realizations devours the Angel, eating its very heart. "She has awakened," cries Ritsuko, referring to the ultimate level of synchronization between pilot and golem (episode 19).

It is Shinji who has awakened. He has realized that he is responsible for his own actions. He is not merely a rider within Eva, he is its pilot, its director. From this point on in the series, he regains free will, taking the initiative in his own growth and healing. Though he still relies on those around him for support, he is no longer terrified of their rejection. The strongest proof of this lies in the last moments of End of Evangelion, where Shinji decides that he will remain separate from the rest of humanity as it evolves into a higher plain of existence that is a near-Angel, returning to Heaven. In this decision, he shows his own self-confidence by not following blindly, and the ability to make choices that satisfy himself by remaining on earth with Asuka, his soulmate. The boy has become a man.