Episode 1: A New Life

The world's nations are beginning to form a new global government. The first OVA is centered around a young girl named Elaine and details the development and creation of a "Genocyber", an ultimate biological weapon created by combining the powers and consciousness of two psychic sisters. The project is directed by a mad scientist and funded by the Kuryu Group (The Kuryu Group was called Kuron in the English dub by Manga UK, but this was corrected by Central Park Media for episodes 4 and 5), a huge Japanese corporation that is a world leader in military research. Starting off in Hong Kong, the story follows Elaine, a nervous young girl. She is central to the ambitions of the scientist who wants to combine her powers with those of her crippled sister, Diana, to activate the Genocyber. Both were children of a former colleague of the mad scientist, whom he betrayed to receive funding for his research.

In its physical form, Genocyber is a gigantic humanoid monster, which the scientist calls a Vajra.^{[lower-alpha 1]} In addition to having almost unlimited strength and regenerative abilities, Genocyber also possesses incredible telekinetic and pyrokinetic powers.

After a brutal search by the scientist and his masked henchmen for Elaine that kills dozens, Elaine is chased by cyborg agents of the Kuryu group, and the scientist is later arrested for going rogue and conducting his own research without the group's approval. During a battle where Diana wears a cybernetic suit of her own to try to catch her, Elaine supposedly dies, which leads to the cyborgs arresting the scientist and collecting Diana. However, Elaine (from within Diana) then uses her psychic power to merge with her and become Genocyber. In the ensuing battle, in which the scientist is killed, huge fires are started, and numerous buildings are heavily damaged, Genocyber also destroys the cyborg agents and throws one of them through a moving airplane. The next morning, Elaine finds that her only friend, a young homeless boy called Rat, whom she met before she was captured, has died after falling from a construction site, likely having been dropped by Wakayama, one of the Kuryu cyborgs. Elaine becomes filled with anger and screams, turning into Genocyber, and initiating a massive explosion which completely destroys Hong Kong, leaving only a barren wasteland in its place.

Episodes 2–3: Vajranoid Attack & Global War

The second OVA apparently occurs shortly after the first one ended. A country called Karain has withdrawn from the United Nations (in protest of the new world government) and launched an invasion of a neighboring country. In response, the United States agrees to deploy a Carrier Strike Group to support offensive operations against Karain. This fleet is to be led by the Alexandria, a massive futuristic Supercarrier stationed off the coast of Japan.

However, satellite photographs have identified an unknown superweapon believed to have been deployed by Karain (in fact, the image is of Genocyber, which destroyed several helicopters after they attacked and killed Elaine's friends). Concerned about the power of this new weapon, the United States military requests assistance from the Kuryu Group. Realizing that the image is in fact of Genocyber (although this is kept secret), the Kuryu Group agrees to send a team of its top scientists to the Alexandria. The Kuryu scientists, including the mentally unstable Sakomizu, bring on board their own secret weapon, a newly created Vajra, out of anticipation that the fleet will encounter Genocyber.

Unlike Genocyber, this new Vajra has a completely robotic body that enables it to almost literally fuse with any machine or weapon it operates. This is demonstrated when the Vajra fuses with a fighter aircraft, enhancing the fighter's capabilities far beyond anything that would be possible for a human pilot.

As the fleet travels from Japan to Karain, the Vajra is conducting a test flight in a fighter when a UN scout plane operating near Karain radios in and requests to make an emergency landing. The pilot also has aboard a civilian he rescued near Karain: Elaine. As the scout plane approaches the carrier, Elaine senses the Vajra, which in turn senses Elaine. Alarmed, the Vajra's fighter veers wildly off-course in pursuit of the scout plane, entering into a steep dive and narrowly avoids crashing into the carrier. The scout plane is forced to make a crash landing on the carrier deck, although Elaine survives unscathed and is taken into the care of the crew.

The carrier's senior officers sharply rebuke Sakomizu for the Vajra's strange behavior, yelling at him that his Vajra is not only dangerous, but is also uncontrollable. Later, Sakomizu yells at the Vajra for embarrassing him.

Unlike in the previous OVA, Elaine now has a largely cybernetic body from the neck down. Although it is unclear why and how this change occurred, it is possible that Elaine and Diana (whose body was cybernetic) have completely merged.

A young female doctor, Myra, takes Elaine under her protection and gives her the name Laura. To Myra, Laura/Elaine reminds her of her own daughter (also named Laura) who died in the plane crash depicted in the first episode of the OVA, when Genocyber was fighting with the Kuryu cyborgs. Although Elaine is still mute, she is able to communicate telepathically with Myra, with whom she forms a special bond. Almost immediately, Myra comes to think of Elaine as her own child.

Neither Myra nor the crew are aware of the girl's psychic abilities and her presence on board is briefly uneventful. However, numerous members of the crew begin experiencing nightmarish hallucinations and several suffer mental breakdowns. Soon after, the Vajra again senses Elaine, and interprets her presence (i.e. Genocyber's presence) as a threat to itself and the ship. Elaine also senses the new Vajra, and, after seeking it out, transforms into Genocyber and destroys it, but Genocyber's arm is hacked off during the fight. The ship's crew, unaware of what actually happened, simply conclude that Sakomizu's Vajra has malfunctioned again, and blame him for the incident (once again, Elaine survives without injury). However, Sakomizu, upon seeing his Vajra destroyed, is insulted and wrongly concludes that the crew sabotaged his work, although he now clearly suspects that Elaine is more than she appears to be. He eventually creates a new Vajra after acquiring Genocyber's severed arm but is unable to control it; the Vajra then expands throughout the carrier, engulfing and consuming the entire crew, except for Myra, whom Genocyber saves. Sakomizu also appears to survive initially, before he too is consumed by the Vajra.

Genocyber then flies into the carrier and reaches the core of the Vajra. The Vajra attempts to fuse itself with Genocyber but Genocyber's psychic powers prove to be stronger, and the Vajra loses control of his body and the consumed carrier, which detonates in a massive explosion.

Later, Myra is rescued by a Karain helicopter as its pilots investigate the remains of the American fleet. Deciding that Myra is delirious, they fly back to Karain, but are horrified to discover that the entire country has been devastated. Genocyber then rises in the sky and spreads its wings, confirming that Karain has suffered a similar fate as Hong Kong. The episode ends with Genocyber flying away, as Myra, who has been driven to madness by the events, yells for Elaine, who she now truly believes to be Laura, to come back to her.

Episodes 4–5: Legend of the City of the Grand Ark, Part I and Part II

The fourth OVA onward are much different from its previous ones in terms of setting, taking place in a post-apocalyptic earth, in a region called the City of the Grand Ark.

The young girl, Elaine, does not appear much in this episode, only a transparent image in the story. In this story, Genocyber eventually realizes that "there was no place in the world for its power" and is dormant until it reawakens at the end.

In a brief opening scene, the now-extremely elderly leader of the Kuryu Group is seen looking at a wall of computer screens that show Genocyber on a rampage of destruction. It is revealed that for 100 years, humanity has been waging a desperate and hopeless war against Genocyber, which has devastated the Earth. He vows to find some way to stop Genocyber, even if it takes centuries. All of a sudden, Genocyber attacks his location, and a massive explosion is seen to rise into the Earth's atmosphere. The next scene, apparently set further into the future, shows a massive space station, possibly a colony ship, orbiting Earth. Aboard the station, a computer monitor indicates that it is now the year 2400 AD.

The story starts out in Ark de Grande City (City of the Grand Ark), one of the last remaining cities on Earth, which is controlled by an evil mayor who claims that he is restoring the civilization that was destroyed by Genocyber, but only does this to gain trust from the civilians. The Mayor is ruthless, killing anyone who opposes him, and most of the city's population lives as an exploited labour class with few rights, while the mayor and an upper class live in luxury.

The story shifts to a couple, Ryu and Mel. Ryu is trying to find a doctor good enough to cure Mel's blindness. They arrive in Ark de Grande City but, as members of the lower class, are unable to get the medical help necessary to allow Mel to see again. Ryu and Mel attempt to earn money as performers, as Mel possesses an extraordinary ability to determine appearances, colours and numbers, even though she is blind. She describes her power as an ability to "see the person's form floating in [her] mind." She also has remarkable hearing and can often sense the environment around her. Ryu has an ability to throw knives while blindfolded, and hit targets with pinpoint accuracy. After Ryu and Mel make love that night, Ryu says that he hopes to earn enough money so that they can leave the city as soon as possible.

Later, Ryu is recruited by a member of the upper class to perform at his establishment, promising a large sum of money. However, the man tricks Ryu (who is blindfolded) into throwing knives at a real person who is tied to a wall, killing him, much to the delight of the spectators. Realizing that he has been tricked, Ryu manages to escape but is now pursued by the city's guards. While Ryu and Mel try to hide in the ruins beneath the city, Mel hears Elaine's voice calling to her, and she and Mel find themselves in a ritual chamber with the seemingly fossilized head and torso of Genocyber at the centre of an altar.

A flashback then shows Genocyber on his rampage of destruction. An image of Diana appears, and her voice then calls to Elaine, telling her that "It has to end. We can't stay in this world. We can't use our power". The two sisters then join hands and disappear, while Genocyber appears lying on the ground, having seemingly been turned to stone. The scene shifts back to the present and to a shot of the massive space station orbiting the Earth.

In a series of images, Mel is seen walking with Diana towards Genocyber's broken body. An image of Elaine appears in front of Genocyber, and Diana screams. In a subsequent dream, Diana refers to Mel as "big sister."

The scene shifts back to Mel, who is taken in by the religious sect which opposes the mayor. The sect believes that the destruction brought by Genocyber was a punishment from God, and believe that Mel is God's messenger, who will prevent such destruction from happening again. Meanwhile, Ryu makes his way up to the surface, where he is detained and subject to brutal interrogation by the police, after which he is apparently declared brain-dead. As Mel worries about Ryu, it is revealed that she is pregnant with his child.

Under orders to destroy anyone opposing the mayor, the city's troops then attack the sect's church, killing everyone, including (apparently) Mel, whose bullet-riddled body lies on the ground with the bodies of children surrounding her.

In an apparent dream, Diana begs Elaine not to turn into Genocyber again, stating that "Our power has no place in this world." Mel, who appears to be in some sort of cocoon, asks Diana for help, stating that if she dies, the child she is carrying will never be born. She also states that she wants the city destroyed. Diana warns that asking for such power will unleash Genocyber, but it is too late: Genocyber awakens as Elaine, Diana, and Mel amalgamate into a red version of Genocyber, one which is much larger than its previous form. As Genocyber emerges, monitors aboard the orbiting space station switch on and begin recording the event. Genocyber then attacks the city, killing the mayor, and then all of its citizens. By the time Genocyber's rampage is over, the entire city has been left in ruins.

As Genocyber rises into the sky, whole pieces of the city's remains begin to tear away from the ground and rise into the air. Genocyber resurrects Mel and Ryu, and Mel is then torn from Genocyber; she and Ryu begin to slowly fall into the burning city. Genocyber then reverts to its earlier, smaller form, and images of Elaine and Diana are seen superimposed against Genocyber as it ascends into the sky. Genocyber then flies into space and attacks the orbiting space station, whose defenses open fire on Genocyber, but with no effect. Genocyber breaks into the station and watches a repeating broadcast of Genichiro Kuryu, the former leader of the Kuryu group, ordering his forces to destroy Genocyber. Diana's voice then calls to Elaine, and images of the girls superimposed against Genocyber are briefly seen before Genocyber begins to freeze itself and the entire space station. The station then falls out of orbit, and explodes as it enters the atmosphere.

The last scene shows Mel, who is no longer blind, and Ryu, lying unconscious in the ruins of the city. As Mel opens her eyes, she hears Diana's voice calling, "Big sister...", and the scene turns to the ruined body of Genocyber, while a baby is heard crying in the background.

A series of stills are interspersed with the main credits. They seem to show that Mel brought up her dark-haired, son alongside a blonde girl - a reincarnation of Elaine and/or Diana?