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Neon Genesis Evangelion

The Neon Genesis Evangelion manga is based of its anime predecessor. The anime was produced by studio Gainax and created by Hideki Anno. While the manga was done by the animeís character designer Yoshiyuki Sadamoto. Surprisingly the manga is still running in Japan, as well as being releasing in the States.
So far in the manga... Since arriving in the super-technological city of Tokyo-3, 14 year old Shinji Ikari has been through a great deal. Reunion with his estranged father Gendo Ikari, head of the classified United Nations agency, NERV. Sudden recruitment into piloting NERVís top-secret weapon, the Evangelion Unit 01, against the mysterios invaders code named "Angels." And not least, exploring a brand new social life with his mysterious, withdrawn fellow Evangelion pilot, Rei Ayanami and the two faced Asuka Langley Soryu. Meanwhile, NERVís tall, dark and handsome Ryoji Kaji (who accompained Asuka to Japa from Germany) has presented Gendo with a very special cargo: a tiny, embryonic object code named "Adam." But does Kaji know about Gendoís decision to digitally "copy" Reiís persona into an experimental "dummy plug" system, designed to deceive an Eva Unit into thinking it has a pilot inside.

Shinji feels a strange connection to Rei, for some reason

Now it has also become clear to NERVís senior officers that Kaji is acutually a double agent, working for the Japanese Minstry of the Interior as well as NERV. After the spy reaveals to both Shinji and Misato the sub basement hangar where NERV keeps the now monstrously grown and incomplete Adam, Kaji decides to go further. He tells Shinji privately what heís learned: that Gendo knew, based on hermetic prohecies from the Dead Sea Scrolls, exactly when the Second Impact wold occur, and that he recieved that information from SEELE, an obscure society that may have been the secret force behind world history. Most disturbing for Shinji is that Kaji prompts him to remember that as a small boy, he witnessed his motherís horrific disappearance during the creation of the first Eva Unit, her invention, not Gendoís. In Nevada, at the one of the two American NERV bases, the Eva Unit 04, under construction, explodes together with its base, leaving a vast crater. Cause, unkown, although NERV suspects it happened during an attempt to load the experimental S2 engine onto Unit 04. Following the disaster, the NERV base in Massachusetts requests their own Eva Unit 03 be transferred to NERV Matsushiro in Japan for its startup test. As Gendo prepares to report the Nevada affair to SEELE as a simple accident, the time has come to pick Unit 03ís pilot.