In a post-apocalyptic world, the last remaining human settlement in Japan is the heavily fortified city of Tokyo-3. Fourteen-year-old Shinji Ikari is brought to the headquarters of NERV, an underground organization lead by his estranged father, Gendou. He requests that Shinji become a pilot of an Evangelion, a colossal android built to fight against monstrous and destructive alien creatures known as Angels that wreak havoc on the planet and threaten the survival of the remaining human race. Although initially reluctant, Shinji is swayed by the idea of reconciling with his father, and agrees to aid in mankind's perilous endeavor against its alien threat, as the pilot of Evangelion Unit-01. Thrust into the midst of a dangerous battlefield, Shinji must find the necessary courage and resolve to face against the Angels' incursions before it is too late.

When the threat of the Angel menace escalates, mankind's defense force is pushed to its limits, with NERV at the forefront of the struggle. Shinji Ikari and his partner Rei Ayanami are assisted by two new pilots: the fiery Asuka Langley Shikinami and the mysterious Mari Illustrious Makinami. With the aid of their mechanized Evangelion units, equipped with weapons perfect for engaging their monstrous opponents, the four young souls fight desperately to protect their loved ones and prevent an impending apocalypse. But when startling secrets are brought to light, will the heroes' greatest challenge prove to be the monsters...or humanity itself?

Following NERV's failed attempt to retrieve the Spears of Longinus and carry out the Human Instrumentality Project, the destruction caused by the Fourth Impact has been largely averted. In a state of disarray, Shinji Ikari, Asuka Langley Shikinami, and Rei Ayanami travel to Village 3—a survivor settlement free from Earth's ruination. There, Shinji slowly comes to terms with his past, developing an entirely different life from his days as an Evangelion pilot. Meanwhile, NERV makes preparations to continue the Instrumentality Project by means of a new Impact. When WILLE's main aerial battleship arrives at the village, Shinji decides to board, believing that he can help by piloting an Evangelion. As new secrets are uncovered and a battle between WILLE and NERV approaches, the future of Earth hangs in the balance. Can Shinji save humanity and the rest of the world one last time?

After being hit by a truck in the year 2014, Akira Natsume awakes to find himself inside a machine following a 16-year-long coma. As he adjusts to the new interface, he is greeted by police officer Minami Uezono and her android partner Alma. The pair shows Akira that his brain is contained inside a device called an EX-ARM—a weapon of mass destruction. Aboard an enemy smuggler ship, the three must escape using nothing but their ingenuity and combat skills. While initially reluctant to fight, Akira soon recalls his brother's words from before the accident. The memory inspires him to take action, possessing Alma's body to fight his opponents using martial arts. Once Alma plugs him into one of the ship's ports, he discovers the devastating potential of his EX-ARM by effortlessly hacking and assuming control of the vessel. Upon safely arriving back on land, Akira meets the other members of the EX-ARM Countermeasure Prevention Team, a police division working to mitigate the effects of EX-ARMs. Witnessing the atrocities committed by those who seek the power of EX-ARMs, he resolves to join the team and put an end to the terror caused by these weapons.