In Episode 1, we are introduced to the Genocyber--A super-powerful monster created from two psychic sisters by a government experiment. The Genocyber's creators promptly loose control of it and it proceeds to run amok, destroying everything in its path (including Tokyo).
In Episodes 2 and 3, the Genocyber project gets moved to a massive battleship, where the mysterious girl from which it came shows up and is taken in by the Ships doctor, who lost her daughter in a plane crash. The Genocyber again proceeds to run amok, destroying anything and everything around.
Episode 4, Legend of Ark de Grande, part 1: At the beginning of this episode, we find that our friend the Genocyber has been causing some pretty serious havoc, and seems to have more or less wiped out civilization in the process of fighting (and destroying) every army in the world, before finally being destroyed some time during the 24th century. The story begins at the beginning of the 25th century, with two new characters; Mel, a blind psychic girl, and Rin, her boyfriend. The two of them are visiting one of the last bastions of civilization, the city of Ark De Grande, to try and have Mel's eyesight restored. After making money on the street for a while, they find themselves in trouble with the law, and end up in the ruins of the last city to stand on this site, buried under Ark de Grande. There, we find out that this also happens to be the final resting place of the Genocyber, and that an underground cult (both literally and figuratively) now worships it as a god, and waits for their "God" to return and cleanse the city.
Episode 5, Legend of Ark de Grande, part 2: In the second half of this new story, Mel has been adopted by the cult as some kind of harbinger. The despotic rulers of the city decide, as they prepare to celebrate their city's 50th anniversary, to wipe out the cult. Meanwhile, Rin has become amnesiac, and is captured and tortured by the authorities. The death squads show up in the underground hideout, and Mel, who has developed some kind of rapport with the Genocyber, asks it for vengeance, initiating the final conflict with what's left of the Kyuryu Group's forces.