Shinji Ikari wakes up to a world unlike the one he once knew: NERV is lost to time, Misato commands Anti-NERV Force WILLE, and Shiro is nowhere to be found with hints of his disappearance pointing to the organization dubbed NEVEC. It's now up to Shinji and the friends he makes along the way to fix his past, and uncover the truth about SEELE and the Human Instrumentality Project.