SEELE orders an all-out attack on NERV, aiming to destroy the Evas before Gendo can advance his own plans for the Human Instrumentality Project. Shinji is pushed to the limits of his sanity as he is forced to decide the fate of humanity.

At the turn of the century, the Angels returned to Earth, seeking to wipe out humanity in an apocalyptic fury. Devastated, mankind's last remnants moved underground to wait for the day when the Angels would come back to finish the job. Fifteen years later, that day has come... but this time, humanity is ready to fight back with terrifying bio-mechanical weapons known as the Evangelions. Watch as Shinji, Rei, Asuka and the rest of the mysterious shadow agency Nerv battle to save earth from total annihilation.

While visiting Hachijo-jima, Conan sneaks aboard a security boat heading to the Pacific Buoy, an off-shore facility constructed near the coasts built to connect surveillance cameras used by police forces around the world. However, an engineer gets abducted! An eerie sound of a propeller hums underwater as a dark figure begins to creep toward Ai Haibara... When the forbidden Black Box is opened, the sealed-away past will surface above the treacherous waves!