The magic/technology described in the story draws upon ideas from Buddhism, Taoism, ancient Japanese myth, element of cyberpunk, Yin/Yang mysticism, and particle physics, with a heavy dose of Shirow's wild imagination. The story is based on minor empire within the expansive (25 world) Galactic Empire, known as Great Yamato Empire, located on minor backwater world. Dealing with gods, end of world scenario and numbers of characters caught up with universe shattering event.
The main plot revolves around the Yamata Empire's plan to destroy all the galaxy's negative karma using a massive technological reactor called the Nāga Generator. Unfortunately, negative karma cannot simply be destroyed, it must be atoned for. However the leader of the powerful mystic Buddhist Fuze Clan plans to stop the destruction of the negative karma which will end up creating the nine-headed Nāga and destroy the world if not the whole universe. To help in stopping the creation of the Nāga, the clan summons a Shinto god known as Susano, the Warrior God of Destruction. The powerful, arrogant, and homicidal god faces challenges. These include the Empire and the clan leader's own daughter, the bratty sorceress Seska, who is possessed by the power of the negative Karma and a powerful magic formula.
At the beginning, the Clan steals a secret magical diagram/formula which contains magic power to control Nāga once it is created.
The clan Fuze's leader, Maître Fuzen, begins the ceremony when his rival, Dr. Hebime, leads troops to the Clan Fuza's shrine to arrest him and his clan. Seska, newly arrived from a starship, is nearly arrested herself and dashes ahead of the troops. She bumbles into the summoning ceremony, and is forced to "wear" the secret diagram on her body to save it.
Dr. Hebime and his troops arrives in time to kill Maître Fuzen and his followers as they complete the summoning ceremony of warrior god Susano Orbatos. Susano warns the troops and is angry that he had no proper offerings to him. Seeing Seska with the diagram on her body, he flattens her completely, rolls her up and swallows her whole. Dr. Hebine forces his troops to attack him and has military HQ fire powerful psycoscience (and forbidden) spells casting weapons at Susano. The weapons strike him and temporary disables him. This infuriates him further and he destroys the Fuze mountain temple as Hebine escapes. Susano resurrects Maître Fuzen and has him witness what happens when a god is angered. He then goes on a rage destroying a good chunk of the capital city. Dr. Hebime summons Hanuman(the Monkey God) whom also fails to stop Susano.
Susano and Maître investigate the palace and discover that Princesse Kushinata is to be sacrificed to the Nāga Generator. They go and fight off the palace's defenses. Meanwhile, Seska is revived by the power of the negative karma and dedicates herself to avenge her father's death and to save her clan by gaining an audience with Emperor. By becoming a royal adviser to Emperor she begins to activate the Nāga Generator and uses the secret scroll which can banish Susano.
Ultimately, the Nāga Generator is activated and both Susano and Seska clash. The Nāga Generator creates a monstrous nine-headed Nāga which becomes so bloated with Galactic Empire's negative Karma its becomes a planet sized Octopus type Nāga. Seska, after beating up Susano, banishes him. As Nāga grows, she becomes fascinated in ruling the Galactic Empire itself.
However, Susano returns, summoning himself, rendering Seska's ability to stop him useless. He enters the Nāga and finds the Princess at center of the generator holding the Nāga force together. He breaks her control of the Nāga and disrupts it.
The giant Nāga splatters over the world like water, flooding it. The Great Yamato empire (what is left of it), sinks under the waves with few survivors. Susaso and the princess leave the mortal survivors of Empire behind wishing them luck. Seska is restored back to normal and is reuited with Commander Ronnel. What remains of Yamato Empire appears to becomes Japan and the world is in fact Earth. However, the story alludes that the Nāga will return.
- Susano Orbatos - God of Destruction: An powerful, Wild, arrogant, homicidal god
- Seska - Bratty, Beloved, Egotistical, bumbling, Sourcress whom is usually an 1st Class Navigator aboard magically powered starships. She has a crush on Commander Ronnel.
- Maître Fuzen - Clan leader of Fuze Clan whom opposes the Naga Generator and summons Susano Orbatos to stop the project. He becomes Susano aid in his crusade to stop the Nāga Generator.
- Dr. Hebime - Leading doctor and creator of Psycoscience and rivial to Maître Fuzen. Creator of the Nāga Generator. Who dedicated to stop Fuza Clan from interfering with his dream of the Nāga Generator.
- Commander Ronnel - Noble handsome officer of the Greater Yamato Empire, and secretly attracted to Seska.
- Sokoku Emperor - Idle, lazy leader of the Great Yamato Empire. Who is approves creation of the Naga Generator and is nearly killed by it.
- Princesse Kushinata - The half-divinity princess who agreed to be scarficed to Nāga Generator to stop negative karma for destroying the Galactic Empire. She has some link to Susano Orbatos.
The Galaxy Empire spans 25 worlds and is connected by magic powered starships.
Masamune Shirow has combined many aspects of magic with technology.
- Elements of cybernetic technology can be seen with in use with warriors the Great Yamato Empire. These warriors integrated with what appear oversize suits of armor which has human's arms and legs, pelvis removed and connected by series wires and tubes. Not all these armors require this, Commander Rommel remains wholly human. These Armor Knights besides wielding swords, staff like Halberds, as well magic wielding devices. These Armor Knights have limited flight abilities.
- Starships - Seen in beginning of the story, Masamune Shirow has starships guided by human navigators which phase through time & space not unlike starships seen in original Dune film of 1984. The warships appear as Japanese warships of Middle Ages which have broadside armarments not unlike 18th century sailing ships warships. These vessels are normally seeing hovering or flying instead of laying in water.
- Diagrams / Forums - These are large circular mystic spells are used by characters of story. They can be used as explosive alarm clocks, summoning spells, magical controlling devices (such as Nāga Generator), as well as controlling starships.
- Nāga Generator - This device was conceived through mixing science and mystic magic to collected all negative karma in known universe to purify the Galaxy Empire.
- Psychoscience - This is mixture of science and mystism which give power wield magic to level of the gods. However, science is needed to monitor and control it this mix. It still being developed, thus prone to problems which are seen through out the story.