Shinobu is first encountered at Santa Destroy High where Travis Touchdown finds her in class, she is initially surprised to be challenged to a Ranking Battle in the middle of class. She tells Touchdown to wait outside while she kills a small group of students who overheard Touchdown challenging her to a Ranking Battle. Shinobu is impatient and seems to want to get the fight over with. However when Travis pulls out his beam katana she becomes angry accusing him of killing her father. It is likely that Touchdown's twin brother Henry was the one who killed Shinobu's father, as it isn't until Touchdown activates his beam katana that Shinobu's overall tolerance of him harshens and she proclaims that she will finally avenge her father, as Henry wields a beam katana similar to Travis'. The two square off, during which Touchdown severs Shinobu's right hand with his beam katana. Touchdown then reveals he had idolized Shinobu's father so much that he watched all of Jacobs' tapes until they wore out, but had never actually met him in person. Shinobu insists he's lying and tells him to kill her, Touchdown ignores Shinobu's cries, opting to spare her life so the two could face each other again in the future.
Although it is implied that Touchdown could not kill her because of his discomfort in killing a woman, and reinforced with his victory against Holly Summers, in the pre-fight phone call Sylvia sardonically defines Travis as nothing but a cold-hearted assassin "...because that is all you ever do. What? Am I wrong?". Travis begrudgingly agrees but Shinobu's actions make him think twice when he realises she is not a killer for superficial reasons but for reasons similar to his own: they both want to find who killed their parents. Shinobu later appears with her right hand reattached, to save Touchdown from being killed by Jeane in the climax of his final Ranking Battle after it is assumed Shinobu had followed Travis in secret to learn of his reasons up the ranks. This 'kindred spirit' relationship would play a profound part in shaping her for the sequel.
In the three years between No More Heroes and Desperate Struggle, Shinobu has become the most prestigious assassin in Asia. She reunites with Travis after he defeats Dr Letz Shake, showing him her belt she won from her fights in Asia and revealing that Sylvia told her to come back to Santa Destroy and help Travis out. Travis claims it's his war and that he doesn't need help, but Shinobu says it's too late for any changes to be made as she has already killed two other assassins, the first being Million Gunman. Before her ranked fight with New Destroyman, she visits Bishop's grave, and meets his unnamed friend. He gives her a mysterious gift for Travis, which is later revealed to be the ROSE NASTY. Shinobu then proceeds to her next ranked fight with New Destroyman. After her fights, she finishes explaining how she defeated the two assassins and then attempts to seduce and kiss Travis. Travis rejects her advances, claiming that he "[feels] like that pervy teacher in a porn", showing his discomfort for taking advantage of a subordinate. He tries to get her to stay afterwards, but she sadly leaves.
In Travis Strikes Again: No More Heroes, Shinobu tracks Travis to his trailer in order to have a duel with him, only to be interrupted by Bad Dog, killing the mood. She then constantly visited Travis. In one of those visits, Henry Cooldown shows up with two members of the 'Order of the Emerald Night', having stalked Shinobu to the location of his trailer. Travis, not wanting to cause a ruckus on his trailer, suggests another place to fight Henry's goons, Shinobu suggests to go to her dojo. She explains that she started teaching martial arts and the ways of Bushido to kids to lead them to a righteous life and that she maintains the dojo with money from assassination jobs. Travis shows concern and asks her to never let kids know about her jobs.
In No More Heroes III, Shinobu takes up residence in the No More Heroes motel, with Bad Girl as her roommate. As FU and the Galactic Superhero Corps begin their invasion of the Earth, Shinobu emerges from her room alongside Bad Girl to join Travis as they prepare to fend off the alien invasion. When FU accosts the group at the motel, he incapacitates Travis with a kick to his torso, and even punched a hole through it. Shinobu attempted to attack FU, but was quickly defeated by him, who proceeded to crush and tear both of her arms off, screaming in sheer agony from the pain. FU then stomped on her head relentlessly and as he's about to kill her, Badman intervenes and strikes FU in the head with his baseball bat, only for FU to then kill him by crushing his head.
As a result of her severe injuries at the hands of FU, Shinobu was placed in a critical coma and is tended to in Naomi's Lab. When visiting her, Travis is clearly troubled upon seeing her, practically begging for her to make a full recovery after she had both of her arms crushed and ripped off by FU. Shinobu remained in her comatose state for quite some time, but eventually recovered from it, now outfitted with two prosthetic arms.
Sometime during her recovery, she hung out with Travis and Bishop as they were doing a Miike and Hideaki viewing party. Travis asks Shinobu how her arms are doing, in which she responds to him that slowly but surely, she's getting used to the sensation, but she's unable to wield her sword until she feels attuned with her prosthetic arms. Travis tells her that there's no need to rush her recovery, but she tells him that she wants to hurry up and help him. Bishop then asks Shinobu what she likes, and Shinobu responds to him that she likes her master, Travis. Bishop remarks that she's a real straight-shooter, but Travis retorts, saying that what he actually meant to say to her was what kind of movies she likes watching. Shinobu tells him that she likes watching G-style stuff, to which Bishop was immediately enthusiastic at her response and assumed at first that she liked Gundam-type movies such as Te**a Fo*ma*s, with Travis asking her if she saw the original or if she saw the film first before seeing the original. However, Shinobu is confused by what they are saying and said to them that what she meant by G-style is something like Barbatos swordplay. Travis now understood her specific type of movie preference, and asked if she was trying to get some practice in. She tells him that she is and that the broadsword action is especially helpful. Bishop remarks that she's a real studious one, with Shinobu telling him that her way is the way of the sword. Travis is amazed by the line, especially for times like these. Bishop then tells him that the "Miike" and "swords" relates to one of Takashi Miike's films, Bl*de of the Imm*rtl, to which Shinobu tells them that she loved the original and would like to watch it, pleading with them to show her the film.
As Travis is making his way to Damon Tower to confront FU, he is joined by his allies, including Shinobu, who has fully recovered and is able to wield her sword now after being fully accustomed to her two prosthetic arms. During the fight against FU, he is gradually weakened by Travis and his allies. Eventually, after Travis lands a lariat on FU and breaks his neck with a vertical suplex, Shinobu and Bad Girl get their revenge on FU, with Bad Girl sending FU up in the air after hitting him with her baseball bat, and Shinobu decapitating him with her sword, causing him to physically and mentally revert back into a child. Damon Riccitiello then betrays FU by blowing him up in his own ship when he attempted to retreat back to his home, killing him.
After Travis defeats and kills Damon, Shinobu is present alongside the rest of the group at Badman's funeral at sea. After Travis and Bad Girl deliver their eulogies, Bad Girl scatters her father's ashes overseas, and Shinobu and the rest of the group throw flower pedals overseas. Afterwards, FU's father, Jess Baptiste V, arrives on Earth alongside his alien armada. As he's about to begin his invasion of Earth, he is suddenly killed in seconds by future versions of Travis and Sylvia's children, Hunter and Jeane, and Native Dancer, who is revealed to be Scott Touchdown, the son of Jeane and the grandson of Travis and Sylvia. Bad Girl asks who are they, with Shinobu responding to her that they are the twin children of Travis. Hunter, Jeane, and Scott explain to the group that Henry killed Travis in the future and teamed up with an alien force to destroy the planet, and asks Travis to join them to help them change the future, much to his bewilderment.