The story starts at the end of the TV Series / End of Evangelion movie during the 'Third Impact' where the protagonist, Shinji Ikari, has been 'complemented' into the 'sea of LCL'. But as the controlling person of the process, he is given a choice by the catalysts of the Third Impact, his fellow Eva pilot Rei Ayanami and the Second Angel Lilith, after he rejects this single person being as a lie, asking for a chance to live his life as a single person.
Either misunderstanding or understanding Shinji better then he knows, Lilith/Rei send him 'back' to the start of the TV series, during the Third Angels attack on Tokyo-3. With full knowledge of what has happened and what is yet to come, Shinji decides, for the sake of those he loves, to pilot the Evangelion one more time and find a way to prevent the future he had seen, from coming to pass. Which in turn places him directly in the path of his Father, Gendo Ikari, his backers in SEELE and the Angels themselves.
The fanfic is in progress. To this date, 13 chapters have been written comprising over 200,000 words.