Two pairs of young lovers become embroiled in a war between two rival kingdoms, the primitive but resplendent Isa and the militaristic but undisciplined Paro. Izu and his young wife, Marin, are simple farmers who live in the unassuming village of Saki, which lies directly between Isa and Paro. While Saki does not have the beauty of Isa nor the war machines of Paro, they do possess a magnificent tree known as "Windaria," to which the villagers give their prayers in return for "good memories." When the war erupts, Izu decides to join Paro's army, enthralled by the fantastic motorbike "given" to him as a bribe. Before he departs, they each take a vow: He will definitely return to her, and until he does, she will wait for him. The other two lovers are Jill, the prince of Paro, and Ahanas, Princess of Isa. They initially want nothing to do with the rapidly escalating conflict, but after Jill's father, Paro's king, dies by his son's hand in an altercation over the war, Jill has little choice but to realize his father's final wish: the taking of Isa. The only problem is that he had promised his beloved, Ahanas, that he would not become involved. Windaria is a war parable set in a fantasy land of unicorns and ghost ships.

A psychic ninja fantasy suggesting that the assassins did not die out during the Sengoku era but burrowed under Japan, where they fought a new war against the alien occupants of a crashed spaceship that has lain undisturbed for several millennia.

In the far future, the elevated irradiation from the sun has destroyed the environment of the earth and the birthrate of humans has drastically decreased. The government controls society with an army of cloned soldiers called "Ideal Children (IC)". Sam Coyne is a trader in a desert. One day, he saves a beautiful woman Maya, who has been chased by Theseus, a corps of IC. He shelters her in his trade ship, but the destroyers of Theseus surround Sam and Maya.

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.