THOMAS CHESTER, a Pinkerton-type detective looking for a reason to live, is assigned to VIP security coverage for a secret product demonstration. On the job, he witnesses a young woman reveal a body covered in gold wires designed to generate electrical energy through a method called seishin-hatsuden, or soul-generation, the byproduct of which is a mind-numbing field called the Shroud which leaches the neurochemicals from people nearby. The woman is SAYURI UEICHI, heiress to the Ueichi mega-conglomerate, inventors of hatsuden. Her implants are unique, however, in covering most of her body and giving her powers that border on the superhuman, something which was previously thought impossible.
The demonstration is interrupted by assassins from Genji Heavy Industries, a rival conglomerate, who kill Sayuri’s parents and attempt to abduct her. Thomas helps her escape, but they are stopped by a man named PERSIMMON, who reveals Thomas has been framed for the assassination. Sayuri teleports them to safety using her hatsuden but is seemingly disoriented and tired from using so much power. With nowhere else to turn, Thomas takes Sayuri to a brothel where his friend and ex-lover, MILLY DRAKE, works. The three of them slip away in the night after evading the police and decide to take Sayuri downriver to the port city of éstfyr. On the way to charter a boat, Sayuri is exposed to the Shroud and is horrified by it. While Sayuri grapples with the horrors of her own clan's make, Thomas is approached by a river boat captain named SHUUICHIRO. They are pursued downriver by Genji and Sayuri reveals her secret to Shuu by turning Shuu’s boat invisible.
Suspicious of the man’s lack of surprise, Thomas confronts Shuu and he confesses that he is a government agent working to prevent Sayuri from falling into conglomerate hands and claims her family members wants to kill her to usurp the conglomerate presidency that she would inherit. Thomas agrees to cooperate with Shuu, keeping this a secret from Sayuri. The next day they find the Genji flotilla destroyed by Kintoki Arms Services, an ally of Sayuri’s family. Open warfare among conglomerates has begun.
The four of them dock at Thomas’ hometown of Burnehithe which has been gentrified by Sayuri’s people. While there, an ?frian—Thomas’ ethnicity—goes on a shooting spree and Thomas is mistaken as a conspirator and taken in by the police. Sayuri goes to rescue him, but Persimmon, who seems to be acting independently of Genji, arrives first. They narrowly escape when Sayuri uses her hatsuden to turn Thomas into a super-powered human shield through means that neither of them understand.
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Back on the boat, Sayuri realizes how dangerous she is and makes a vow to be useful. Shuu teaches her how to pilot the boat and Thomas teaches her how to fish, but the closeness is ruined when Sayuri treats their relationship as contractual. Along the way they help recover a baby stolen by river pirates and upon returning the child are warned by some villagers that there is a general strike about to happen in éstfyr in protest of the conglomerates and that it might turn violent. With no other option, however, they elect to go anyway.
As Sayuri's party nears éstfyr their boat is held up by Kintoki soldiers who insist on taking Sayuri despite her resistance. In a desperate attempt to buy time, Shuu reveals himself to be a government agent, but the commander has been given orders to take Sayuri no matter what and Shuu is killed in the ensuing fight. Sayuri pilots the boat to éstfyr in the middle of a strike against Kintoki.
With the Shuu's secret exposed, Sayuri becomes convinced Thomas wants to get rid of her by turning her into the government and runs away. She is caught and kidnapped by a young dockworker named LEOFSIGE 'SIGGY' ?LFR?DSON who believes she’s a conglomerate spy and takes her into the Grand General Union of Workers (GGUW). They quickly discover her hatsuden and the union leadership decides to kill her so the conglomerates cannot have her and her technology. Siggy convinces them not to kill her and to let her help them, with Sayuri agreeing provided isn't asked to use her hatsuden for violence.
Sayuri joins the protest right as Kintoki deploys the Shroud to pacify the striking workers. She uses her hatsuden to cancel out the Shroud but to her horror this results in violence as the workers storm the Kintoki armory. Genji uses this opening to launch an attack on Kintoki, shooting down their aircraft and killing protestors. Sayuri heads for the roof of the armory.
Thomas catches up with her and tells Sayuri he will continue to protect her no matter what because it is his reason for living. As they reunite, Persimmon arrives and threatens to kill Thomas to keep Sayuri from teleporting. Double-crossing Genji, Persimmon wants Sayuri to help him subjugate the conglomerates under military rule and re-stablish the warlord governments of old. While threatening them, he shoots off Milly's arm. Sayuri realizes that her special hatsuden is a curse which implicates her in violence whether she uses it or not and decides she would rather be an active participant. She kills Persimmon and knocks out electrical power in the city, crashing the Genji planes.
The next morning, Sayuri visits the GGUW leader, OLIVER MARTIN, and despite her reservation about their politics, she agrees to join them as the best use of her hatsuden. The story picks up the same day.
