Somewhat based on the real story of how Gainax was founded, Otaku no Video addresses all aspects of an otaku lifestyle. Ken Kubo is a young man living an average life until he is dragged into a group of otaku. Slowly, he becomes more like them until he decides to abandon his former life to become king of otaku—the otaking! Mixed in are live-action interviews with real otaku, addressing every aspect of hardcore otaku life. Not only are anime and manga fans included, but also sci-fi fans, military fans, and other groups of Japanese geeks.

Mayfly reveals Cima's backstory in flashbacks as she reflects on her past prior to the events of Episode 13. It reveals that Cima and her unit poisoned a Side 5 colony using G-3 nerve gas, under orders, but were treated as pariahs afterwards by their own countrymen for committing such an atrocity. At the end of the war her superior refused to let her retreat to Axis. Because their home colony Mahal had been converted into a weapon, Cima and her men were left stranded and homeless.

A.D. 2040—Thirty years have passed since the battle between the Earth and Zentraedi forces changed the lives of both races. On planet Eden, a top-secret project known as "Supernova" is being held to determine U.N. Spacy's next-generation variable fighter. Competing to win the funding are Shinsei Industries' YF-19 and General Galaxy's YF-21. Piloting the YF-21 is Guld Goa Bowman, a half-human, half-Zentraedi. Shinsei receives its new test pilot in the form of the unruly fighter pilot Isamu Dyson, who was once a friend of Guld. Meanwhile, as Isamu and Guld furiously battle to see which of their fighters is superior, a Virturoid Idol named Sharon Apple is to perform her debut concert on Eden. In charge of Sharon is producer Myung Fang Lone, another former friend of Isamu and Guld. When the three meet each other, old disputes spark from a troubled past. Little do they know that their past incidents—along with the Supernova Project and Sharon Apple—will somehow bring them together.

When you look up at the sky, what do you see? A blue sky? Freedom? A hopeful future? The people of Tokyo see none of these. Instead, an ominous alien mothership looms overhead, engulfing the city skyscape. Three years ago, they came. The arrival of the "Invaders" sparked the greatest war humanity had ever faced—one that threatened to end the world. The Japanese government scrambled to fight the Invaders. Weapons were mass-produced, sparking controversy and pacifist movements. That day, everything changed. And yet, nothing has changed. Kadode Koyama and Ouran Nakagawa live their final days like they always have: going to school, playing with friends, and doing what any carefree high school girl would do. As they grow up they come to learn what it truly means to be an adult, in a world where adults seem to be demons who only deceive and destroy. They come to learn the real threat to humanity is not the Invaders, but humanity itself.