Shinji Ikari, the son of the head of NERV operations, Gendo Ikari, is a loner. Due towards his self-internalization of feelings, he has a hard time interacting with the world around him and oftentimes keeps to himself at school. When his classmates find out that he is the pilot of one of the EVAs, excitement turns to fear and anger. It is only after a series of misunderstandings that Shinji is able to find two close friends, Toji and Kintaro.
Living with Misato, Shinji has a chance to experience something that his heart has always longed for -the touch of a loving family. Through a series of flashback scenes of his childhood this is intricatly revealed. The fact that he once had a mother and now doesn't even mention her name nor her existence -leaves the audience with a mixture of sympathy and curiosity in his silent anguish. His father's avoidence of him also spurns silent compassion and intrigue.
Throughout the course of the series, he seems to be the central and the most complex character. In one sense, Shinji can be seen as a boy who is still trying to find himself amid all the chaos and destruction around him. The loss of innocence brought on by his mysterious past and his position as the pilot of EVA-01 appearantly has had severe mental implications upon him. However, throughout his ordeal, the need for his father's approval is what keeps Shinji from going on to pilot his EVA -even though he hates doing so.
The relationship between Shinji and his EVA is another mystery. Their increasing synchronization, and the fact that EVA-01 protected Shinji from falling debris during an Angel attack -without any power supply has myself intriqued. Unfortunately, this coincidence is never really explained in the series or the movie (so I've heard).
Shinji's growing fascination with the emotionless Rei Ayanami is another curiosity. Whether it is silent love or admiration that he has for her, his fixation with her grows throughout the series. Similar in their solitudes, the two form a bond at one point, but it is quickly destroyed after a tragic accident occurs (son't worry, I won't ruin anything for those of you who haven't seen it!).
At the end of the series, it is Shinji who plays the central role in bringing everything together. Through his loss of innocence, struggle and pain, he shapes the course of humanity and brings a disturbing closure to one of Anime's greatest epics.