"Shinji to be awesome doesn't need to be an asshole. Or be replaced utterly. One simple, simple thing. Just change his childhood. Make him happy. Everything pulls its own weight after that."
—Charles Bhepin, the author.
The concept of the story is that a young Shinji Ikari finds a collection of Warhammer 40,000 books and minatures lost during Second Impact and creates imaginary confidantes and advisors based on several of the figures (an Eldar Farseer, Ork Warboss, Space Marine and Chaos Space Marine). Through their counsel, his character develops in a rather different fashion than canon - although still slight and unassuming, he proves strongwilled and mature beyond his years, making a deep impression on those around him.
When he is summoned to Tokyo-3 to pilot an Evangelion, Shinji quickly becomes a focal point for the simmering resentment against his father and SEELE, both of whom assume that he is a playing piece used by the other in their silent struggle for the fate of mankind. Here, at first drawing on his previous connections and then making new allies, Shinji becomes a figure of international significance. Many of the developments (bolt rifles and titan modules) are drawn from the 40K mythos and there are strong implications that Shinji is taking a role similar to that of 40K's God-Emperor of Mankind.
The Shinji and Warhammer 40K Wiki, wiki set up by fans on Wikia
Tokyo-3 Fortress City Wiki, wiki set up by author on Wikia