A mysterious cell wearing a stylish hat appears before the regular cells, who are bored with just the same (cell division) work over and over again, every day. This mysterious cell lures the regular cells into a mischievous scheme against White Blood Cell and Killer T Cell. The regular cells enjoy working out their everyday, pent-up frustration. But, just who exactly is this cell wearing a stylish hat?

In the year 2015, more than a decade has passed since the catastrophic event known as Second Impact befell mankind. During this time of recovery, a select few learned of beings known as the Angels—colossal malevolent entities with the intention of triggering the Third Impact and wiping out the rest of humanity.

Called into the city of Tokyo-3 by his father Gendou Ikari, teenager Shinji is thrust headlong into humanity's struggle. Separated from Gendou since the death of his mother, Shinji presumes that his father wishes to repair their shattered familial bonds; instead, he discovers that he was brought to pilot a giant machine capable of fighting the Angels, Evangelion Unit-01. Forced to battle against wave after wave of mankind's greatest threat, the young boy finds himself caught in the middle of a plan that could affect the future of humanity forever.

Nan-young is a scientist whose astronaut mom failed to return to Earth when things went awry during her Mars probe. Nan-young has always dreamed of exploring space too and longs to go to Mars in hopes of finding a trace of her mom. Her dream comes true when she is selected as one of the astronauts for a Mars probe project. Before she blasts off though, she meets Jay, a musician who also fixes retro sound instruments. It's all thanks to an old turntable that Nan-young inherited from her mom.

Sequel to .