Gene Starwind and James "Jim" Hawking are hired by a woman named Rachel to protect and escort her as she services farm equipment. When they are attacked by Kei Pirates, they learn Rachel is really "Hot Ice" Hilda, an outlaw in search of treasure. After the pursuing pirates are defeated, Hilda shoots Gene and forces Jim to fetch a large container. The container is opened, revealing a naked girl inside.

The girl in the container is Melfina, who wakes up from suspended animation. Escaping from the Kei Pirates in a drop-ship, Gene, Jim, Hilda, and Melfina go into space. They then take Hilda's spaceship Horus to Blue Heaven, an outlaw hangout. A Corbonite named Swanzo is enlisted to repair and resupply Horus. While Jim takes Melfina shopping, Gene and Hilda go to a bar and get into an altercation with McCoy and his lackeys. As a result, they are attacked that night in their bedroom.

Gene and Hilda defeat McCoy, and the protagonists then escape into space ahead of his men. They get into a game of chicken with a Ctarl-Ctarl ship led by Aisha Clanclan, who ends up destroying their pursuers in a fit of rage after losing. Aisha is demoted after letting the Horus escape and is left behind on Blue Heaven. When the Horus reaches an agreed upon rendezvous point, Hilda finds that the Kei Pirates have killed all her friends. The crew escapes the pirates and they set a course for Farfallus.

The Horus arrives at Farfallus and docks on an asteroid containing the XGP15A-II, an advanced spaceship. Hilda turns on Gilliam II, the computer of the XGP15A-II, which registers the four as its crew. Melfina displays her ability to link her mind with the ship while the Kei Pirates arrive and attempt to gain control of the XGP15A-II. Gene, Jim, and Melfina later escape the star's gravity well, by breaking out of the asteroid, while Hilda sacrifices herself to protect them from the Kei Pirates. Gene names the ship the Outlaw Star in Hilda's honor.

The crew of the Outlaw Star travels back to Blue Heaven and Swanzo agrees to paint and outfit the ship with a registration ID in order to pay a past debt to Hilda. Aisha, now broke and homeless, shows up and demands the coordinates of the Galactic Leyline, which Gene is unable to provide. After Aisha persistently tries to fight them, the crew takes her out to dinner, seemingly out of pity, but Gene ends up shooting her and leaving her with the restaurant bill.

Gene and Jim meet up with an old friend, a wealthy businessman named Fred Luo, who has become the target of a female assassin named "Twilight" Suzuka. Gene agrees to protect Fred in exchange for munitions, and ends up beating Suzuka in a duel. Suzuka agrees to leave Fred alone as long as Gene is alive, and vows to kill him instead.

Gilliam II runs simulations to try to teach Gene how to take off in the Outlaw Star, but Gene repeatedly crashes. Jim gets his car out of impound and goes to work as mechanic while Melfina learns to cook and Gene works on the ship. A Kei Pirate attacks Melfina but Suzuka intervenes, killing him. Meanwhile, Gene's fight with another Kei Pirate leaves him poisoned. The crew then meets up on the Outlaw Star and Suzuka asks to help out because of her dislike towards the Kei Pirates.

Gene becomes unconscious due to his previous battle with the Kei Pirate, who offers an antidote in exchange for their ship. Gene wakes up and declines the offer and Melfina purges the poison by taking Gene into the navigator booth of the spaceship. The Kei Pirate and his robots then attack the Outlaw Star, and Gene and Suzuka defeat them, only to be confronted by three more Kei Pirate grappler ships.

Gene does not take Jim seriously concerning the maintenance of the ship as well as their freelance business. Gene and Jim take on a contract to find and kill a man named Zomba in exchange for 10,000 wong, but they find a cyborg duplicate of this man instead, only being rewarded 2,000 wong as a result. They resolve to find the real Zomba and collect the full reward, but find out that the real Zomba has already been killed by Suzuka.

The Outlaw Star reaches Heifong and the crew enters the Thirteenth Annual Heifong Space Race, with some financial help by a sponsorship from Fred's company, in an attempt to promote Gene and Jim's business, and for Gene to gain more information about the El Dorado, the ship piloted by Ronald "Ron" MacDougall and Henry "Harry" MacDougall.

Gene makes a daring dive into the first checkpoint and avoids the space wave. Aisha abandons her ship and is brought on board, and after finally being convinced that Gene knows nothing about the Galactic Leyline, she decides to stay on the Outlaw Star. The crew finishes the race in fourth place, but first place in the privateer class, and they break even in their deal with Fred.

After the race is over, Gene contacts Harry, who challenges him to a duel between the Outlaw Star and the El Dorado in an asteroid field. The El Dorado later infiltrates the Outlaw Star, and Harry tries to hack into Gilliam II and has interest in Melfina. But it is later found out that Ron is piloting another ship, bringing Harry back with him.

Gene and Jim set up a business on Heifong, and the crew members take on various jobs around the city, which all come together in a confrontation with a mind-controlling cactus and its giant insect servant.

The Outlaw Star is performing a transport job, when the advertising ship they are pushing latches onto them and takes control of their computer. The culprit turns out to be a terrorist named Crackerjack, who threatens to blow up a bomb he has placed on the ship unless Heifong is given independence. While Gene looks for a way to disarm the bomb on the ship, Aisha and Suzuka work on tracking down Crackerjack to save the others on Heifong.

Lord Hazanko gathers six of the Anten Seven together and explains that they will have to kill Gene Starwind. The seventh member, Shimi, later arrives at Starwind and Hawking enterprises and challenges Gene to a duel. Gene meets Leilong at a bar, having a friendly drink together. The following day, Gene realizes that Leilong is actually Shimi, after killing one of his lackeys. The other crew members try to interfere, but to no avail. After a one-shot duel, Gene unexpectedly wins and Shimi seemingly dies.

Gene, Jim, and Melfina are contracted by an old man to recover a shipment of dragonite ore from a ship that crashed on the water planet Heifong VII, which leads to a battle with the creature guarding the ship and its ore. Once the dragonite ore had been loaded onto the ship, the old man sacrifices himself to the creature in order for the crew to safely escape from the planet.

An unknown client, later found out as Ron, contacts the crew of the Outlaw star and asks Gene to meet him at a restaurant to discuss about the Galactic Leyline with its ties to the Outlaw Star and Melfina. Outside the restaurant, Gene, along with Jim, Aisha, and Suzuka are faced again Ron and his dog-like weapons. Meanwhile, Harry attempts to seduce Melfina and steal the Outlaw Star, but to no success.

In exchange for a substantial loan of money from Fred, the Outlaw Star crew enters the Universal Strongman Tournament to stop Fred's fiancee, Reiko Ando, from winning as the strongest woman in the universe, and thus prevent a marriage between the two. Gene, forced to dress up as a woman, enters in the tournament under the name "Jenny", soon winning the match despite his injuries. Aisha, forbidden from competing on the basis of her origin, also enters the tournament under the guise of a masked wrestler named "Firecat". She later fights against and triumphs over a Kei Pirate named Lady Iraga, revealed to be from the same tribe as her.

The Outlaw Star and its crew is captured by private security forces and Gene confronts their leader, a Saurian named Dooes, accompanied by his colleague, Valeria. The security forces attempt to help an injured civilian ship, but it turns out to be Trojan horse. The Outlaw Star and its crew save the security forces and are rewarded with dragonite.

The Outlaw Star battles a mysterious ship and retreats, docking at a nearby outpost for repairs. Jim encounters a pair of cats in a park and follows them to their owner, a girl named Hanmyo, and he goes on a date with her. What Jim does not realize is that the girl is the pilot of the ship that attacked them, and the cats are her co-pilots.

The crew searches for information about the Galactic Leyline in some ruins on a deserted planet. Harry tries to seduce and kidnap Melfina again, but he is rebuffed by Gene. Meanwhile, Ron attacks the others, only to be interrupted by an earthquake. Later at an outpost, Professor Nguyen Khan puts Melfina to sleep with code words and tells Gene to go to a prison for information on the Galactic Leyline.

Gene, taking his position as a prisoner, meets Saiyo Wong, who has the coordinates for the Galactic Leyline. They escape and the man gives Gene a device which he says contains the coordinates. Professor Khan wakes Melfina up, and Gene then kicks Khan off the ship.

The group goes to the vacation world Tenrei so Gene can look for caster shells to prepare for their trip to the Galactic Leyline. The crew relaxes in the hot springs and Gene meets with two priests, Ark and Hadul. They give him the caster shells in exchange for lewd footage of a third female priest named Urt. A side story includes a Kei Pirate named Tobigera, who repeatedly fails to assassinate Gene.

The Outlaw Star, the MacDougall brothers with Khan, and Hazanko and his crew all struggle to make their way into the Galactic Leyline, where they see a cylindrical figure covered in black and gold. Melfina is transported away as a disembodied voice asks them the reason for their return as well as for the thing they most desire.

Suzuka, Gene, and Aisha confront and defeat Hitoriga, Hamushi, and Jukai, respectively. Harry finds Melfina at the gate, but is severely wounded by Hazanko, who commands Melfina to open the gate. When Khan also enters the gate, Gene kills Ron near there, which triggers his memory of his childhood when his parents were alive. Gene later tells Jim to gather Aisha and Suzuka back onto the ship. Harry helps Gene and Khan by opening the portal before passing away.

Upon entering the portal, the Galactic Leyline takes Gene, Melfina, Khan, and Hazanko to cyberspace and revives them, all having their wishes are granted. As Khan acquired all knowledge, Gene obtains Melfina, while Hazanko possesses ultimate power. Gene and Melfina combine their strengths and defeat Hazanko inside the spiral of the Galactic Leyline. In the aftermath, after having gone their separate ways, the group is reunited as the Outlaw Star needs a repair job, and the group is set to head out to another section of space, unknown of their fate.