Before being eventually compiled as one single volume in 2007, the four short stories were first published in Ultra Jump in 1997 and 2006, and three of them ("Furusato", "Seiyakyoku" and "Sonic Finger") had also been included in the Japanese Gunnm: Complete Edition. No English version has been published.
Several characters who appear in the side stories do not appear in the regular manga. The side stories also provide more background on the Factory and motorball.
The first story takes place during Alita's days as a TUNED agent working for Tiphares before she encounters Figure Four. Deckman 50, the sole survivor of an attack on a Factory convoy, sets off in search of water across the desert in response to a dying guard's plea. Alita, lying half buried in the sand, is given the mission to terminate him by Chief Biggot. On her way, she takes great delight in killing various forms of desert life which she comes across.
Deckman 50 eventually reaches the sea, where he becomes the center of attention of a group of children from a nearby fishing village. Alita has him in the sights of a sniper rifle, but does not shoot because of the children. When night falls and Deckman 50 is left alone, he is shot.
The second side story takes place five years before the start of the main story. Ido, recently expelled from the floating city of Tiphares, has taken to working as a hunter-warrior to make ends meet. One cold Christmas night (which only Tiphareans seem to now observe), Ido rescues a young woman from a hulking robot and takes her home. This leads him to getting kicked out onto the streets by the woman he is staying with. Ido decides to name the mysterious woman "Carol" after the Christmas carol, and discovers she has almost complete amnesia and can barely remember how to speak. He and Carol are sheltered by Gonzu, who takes them in out of gratitude for Ido having previously saved his life.
Gonzu puts Ido in touch with the veteran cyberphysician Gauss, under whom Ido serves his apprenticeship for six months. However, used to working with humans, he is unable to empathize working with cyborgs during this time, who comprise the bulk of the Scrapyard's population. Depressed after learning from Gauss that he will not succeed as a cyberphysician otherwise, he is discovered by a fellow Tipharean doctor, Dedekind. Dedekind specializes in transplanting regrown human limbs to replace the cyborg limbs of his clients, and Ido serves under him for six months at his island mansion/clinic. During this time, Carol matures emotionally and intellectually at an exponential rate, becoming fully articulate and learning how to beat Gonzu at chess. Ido's feelings for her also deepen during this time.
After six months, he accepts Dedekind's offer to become his assistant. The same day though, Carol is kidnapped by the same robot she had fled from a year ago. After she manages to contact Ido, he realizes that she is at Dedekind's mansion. There Ido confronts Dedekind, and to save Carol from the robot which comes after her, damages it with his rocket hammer. Reunited with Carol, he suddenly realizes that something about her is wrong. Dedekind reveals that Pakila, one of his clients, had an accident serious enough to damage all of her vital organs except for her brain. Rendered a complete cyborg, she had Dedekind create a clone of her body using her brain cells. The clone however escaped and was rescued by Ido, leaving Pakila trapped in her cyborg body for a year. After kidnapping Carol, her brain was transplanted into Carol's body and Carol's into that of the robot. Her attitude and personality clash with the Carol that Ido has come to know, and she tries to finish off the damaged robot that now houses Carol's brain. However the attempt goes awry, killing Dedekind and hitting a gas pipe in his mansion that sets the whole structure ablaze. As Pakila is killed in the fire, Ido is saved by the robot, which shelters him from falling debris and sets him adrift in a boat as Dedekind's mansion is destroyed. Having sustained fatal damage, the robot too is destroyed.
Ido returns to Gauss a changed man, enabling him to eventually set up his own practice and clinic featured in the main Battle Angel Alita story.
The third side story takes place after Alita's fight with the motorball champion Jashugan and her retirement from motorball. An unnamed man in a bar watching Alita and Jashugan fight on TV sets his beer bottle rapidly spinning on its base with one hand before finishing it off. After the conclusion of the fight, he leaves the bar, later going to the Western Sector of the Scrapyard. Three months later, Alita is shot in the head by a sniper while out on morning exercises, but survives. A group of hunter-warriors led by Teito band together to hunt the sniper down. Alita, fully recovered and out exercising, is invited by a man working for a Factory disposal unit to have tea with him. She does not stay long, but borrows a book from his well-stocked library.
With the assistance of the investigator known as The Nose and the informant Walrom, the hunter-warriors discover that the likely suspect is a hardened criminal known as the Sonic Finger. The Sonic Finger was active in the Western Sector of the Scrapyard, where he killed 37 out of his 43 victims, including the hunter-warrior Macheko. Information on him is sparse and there is no Factory bounty on him, but Alita figures out who the likely culprit is. She sends the man who she had tea with an invitation to fight when she returns his book, which he accepts. After writing up his will, the Sonic Finger equips his specialized cyborg arms and sets off.
At an abandoned Scrapyard factory, the other hunter-warriors are lying in wait for the Sonic Finger as part of Alita's plan. He makes his appearance soon enough, and despite their best efforts, manages to take down in order, Beck, Blu, Tank Man, Skull, and Teito. Facing Alita alone on top of a high section of factory pipe, the Sonic Finger uses his best techniques on her, but is quickly defeated, falling to his death.
This is the only side story set in the Last Order continuity and focuses on Koyomi, who is trying to earn a living as a photographer but without much success after breaking the scoop on the deal struck between Kaos and Vector to build the Tower of Tiphares. Following a tip that Den has reemerged and has been ambushing supply convoys bound for the Scrapyard, she journeys into the wasteland with a convoy in search of Den. The convoy she is with is attacked by Den, but he does not recognize Koyomi, who is injured. She is rescued and cared for by an old eccentric named Geriperi who lives near Farm 3. A week later, Geriperi is apparently killed and Koyomi discovers that Eakins, the head of Farm 3, is responsible for the convoy attacks by using a remote-controlled body of Den. Agreeing to help him with his plan to revive the Barjack for her own reasons, at the revival a large number of Barjack witness a duel between a second Den who challenges the first and defeats him. As he disappears after ordering the Barjack to assist with constructing the Tower of Tiphares, Koyomi begins to find a purpose in life.