Genetically modified dying top female assassin called "044" is hired by corporate government to take out King, the secretive leader of an underground rebellion. She goes to New Tokyo, a space-station-turned-metropolis, to find him.
King sends some men to kill 044, but she quickly disposes of them and tracks down his lair in the sewers. There she fights more of his men, including Luka, who unexpectedly awakens strange feelings in her, so she spares him.
Luka doesn't trust 044 and goes to save his boss King. She feels she must protect Luka, so she follows him. The corporate government's shady representative and 044's boss Daxus II sees this as treason and puts a contract on 044 as well.
Now on the run, 044 still has one friend - her personal physician and friend, Garcia, who asks his old friend Matilda to help them hide themselves and Luka at her clinic for a spell.
The rebels who call themselves the Phage after the disease they suffer from, kidnap Luka from the clinic, just as deadly agent 724, sent by Daxus II, and his forces find them.
Sakuza turns out to be a charismatic veteran of a miner revolt that cost many lives and was eventually drowned in blood. He decides to help 044 and Garcia hide.
Angered by the failure of his men to deal with 044, Daxus II decides to take matters into his own hands and arrives personally at the mining space colony called Coffin of Despair, where 044 is hiding.
044 and Garcia are getting desperate. They need to go somewhere where Daxus II will never find them. While they ponder their next move, Luka reenters the picture.
044 is dying from Phage, a disease vampiric in its nature. She learns there's a connection between her and a fabled female warrior known as Ultraviolet. She attacks Daxus II's headquarters to find her and Luka attacks it to find King.
