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After the second impact, all that remains of Japan is Tokyo-3, a city that's being attacked by giant creatures that seek to eradicate the human kind, called Angels. After not seeing his father for more than eight years, Shinji Ikari receives a phone call, in which he is told to urgently come to the NERV Headquarters, an organization that deals with the destruction of the Angels through the use of giant mechs called Evas.

Under constant attack by Angels, NERV introduces two new pilots: the mysterious Makinami Mari Illustrous and the intense Asuka Langley Shikinami. Parallel to the incursion, Gendo Ikari and SEELE proceed the secret project that involves both Rei and Shinji.

The brothers Elric will consider the answers that are left once the Philosopher's Stone has guided their saga to and end. True sacrifice, the deep love of family, the cruel truths of life and death.