Charden and Kyoko go to Rubeck City, where Gyanza Rujike , an escaped convict who got his power of Tao revealed by the Apostles of the Star, is slaughtering the population. Kyoko finds the town "boring like hell," given that the stores are closed and all the population is hiding from Gyanza They finally meet Gyanza, who attacks them immediately without even making them flich. When the deranged murderer recognizes them, he accepts to talk but refuses to join the Apostles. Gyanza then orders them to leave. He grabs Kyōko's face, saying that her voice must be pretty when crying, triggering the teenage girl's wrath. Hadn't Charden stepped in, she would have reduced Gyanza to ashes, as she is much more powerful than him. Kyoko is extremely irked but Charden merely states that someone like Gyanza would only be an hindrance to them. Shortly after, they feel Gyanza's ki increase, as he is fighting against Train Heartnet and his partners, Sven Vollfield and Eve. (Kyoko feels it as well, though she doesn't pay attention at first.) Upon witnessing Gyanza's defeat, Kyōko congratulates Train for defeating a Tao-wielder with a gun and attempts to reward him with a kiss, only to get whacked on the head. Charden then arrives and introduces the Apostles of the Star to Train's gang.
The following night, as Kyoko and Charden are waiting for the Apostles' airplane in a graveyard, (which Kyōko finds gloomy) they meet Belze Rochefort, the Chrono Number II, (second-in-command of Chronos' elite military brigade) who was tracking them down to dispose of them. Kyoko engages a one-on-one battle against Belze and manages to drive him into a pinch, but he is too strong for her alone and she requires charden's help. As they are about to fight two-on-one, Belze is now in a dire situation but fortunately for him, Shiki interrupts the battle and takes them away.
Kyoko then returns to her country of Jipang, where her head teacher berates her for her repeated absences, but she dismisses his rants and departs to answer Creed's call. She takes part in the high-scale terrorist attack on the World Conference, where among other murders, she jumps on a car and detonates it by overheating the motor. She laters goes to buy toys in a market, dragging Leon along as he seemed bored. When Creed kills Durham, causing Charden to doubt his motives, Charden talks to Kyoko who shares his uneasy feelings, and understands that if she were to disobey, she might get killed as well. Unfortunately for Charden, Kyōko is more interested in seeing his face without glasses.
When the Apostles of the Star are hiding in their castle in the mountains near Stoke Town, Kyoko takes part in the "sweeper's hunt game." She mistakes the thief-for-hire Rinslet Walker for a bounty hunter (as Rinslet was investigating on Creed on Chronos' behalf) and attempts to kill her with a fireball, but Doctor steps in and stops the fight, taking Rinslet into the castle. Later, when Charden defects from the Apostles of the Star, Kyōko goes with him so that he won't be lonely.
They go back to Stoke Town and the following day, they run into Train, Eve and Rinslet. Charden greets them politely and Kyoko proudly announces that they are no longer part of the Apostles of the Star. Kyoko is then taken hostage by a thug with a knife, whom Train knocks out before Kyoko can attack. Train merely caught a criminal as a bounty hunter, but Kyoko persuades herself that he risked his life to rescue her and falls in love with him, much to Train's embarrassment and annoyance. She begins calling him "Master Black" ("Kuro-sama") and manages to get his phone number and e-mail address from Eve. Later, Train is accidently turned into a child by Creed's nanomachines. As he is walking in the streets, he discovers that Kyoko sent him 30 text messages. Horrified, he considers getting back to his hotel before running into her, but she appears right next to him, fleeing from assassins from Chronos. Without listening to Train's protests, she grabs him along to "protect" him. When she resolves to kill the assassins Train tells her that murder isn't something to be taken lightly, before neutralizing the assassins and making them flee. Strongly impressed by "Master Black's policy," Kyoko resolves not to kill anyone anymore, no matter how annoying they are. She then calls Charden, who asks Train to ensure Kyoko's protection.
Unfortunately, Kyoko is targeted by Baldorand Kranz , the Chrono Numbers VIII and IV: two merciless killers, blindly devoted to Chronos. Upon learning that Kyoko is no longer an Apostle of the Star, they not only still seek to destroy her, as she is a Tao-wielder and an international criminal, but also to kill Train, who betrayed Chronos when he left the Chrono Numbers. Train tells an irked Kyoko to respect her promise "not to kill anyone" and tells her that as long as she stays true to her words, he will protect her. Aggravated by the Numbers' attempts on Train's life, Kyoko nearly breaks her promise and attacks Kranz, only to stop in her tracks at the very last second. The battle is ultimately interrupted by the Chrono Number VII Jenos Hazard. Jenos reports the whole story to the Chrono Number I Sephiria Arks, who asks to meet Kyōko before making a decision.
Kyoko is disappointed to learn that Train won't come with her to see Sephiria, but she displays newfound maturity when she refuses his offer of going to her rescue whenever she calls him, stating that she doesn't want him to get involved in her problems anymore.
Kyoko later finds and befriends a black kitten in the streets, whom she adopts and calls Blacky, before Jenos and Rinslet take her to see Sephiria. Sephiria, who knows about Kyoko's promise, decides to test her resolve and carves a gravestone with her sword, telling her that if she doesn't become one of Chronos' assassins, she will be killed outright. When Kyoko refuses, no matter the risks, Sephiria calls off her bluffing and allows Kyoko to go back freely to Jipang.
During the final battle on Clarken Island, Train enters Doctor's Warp World (the alternate universe which he creates and controls with his power of Tao) and is sent to an empty wagon in some underground tube, where he is greeted by none other than Kyoko Kirisaki.
As Train is wondering whether he has been sent to Jipang, Kyoko suddenly takes offense of his refusal to kiss her and attacks him with the intent to kill. Train and Kyoko are then transported to a deserted, misty town. When "Kyoko" attacks him without being bothered the slightest by the change of place, Train's doubts about his foe not being the real Kyoko are confirmed. The giggling Kyoko look-alike then tells him that Doctor trapped him here and sent her to deal with him while he himself is busy dissecting Eve. She then adds that Doctor wants Train to be killed by the people whom he cares about and a doppelganger of his late best friend Saya Minatsuki suddenly steps out of the mist.
Train finds himself trapped in this misty town of which he cannot escape, having to fight two doppelgangers as powerful as the original ones and impervious to any attack, who appears wherever he is, no matter how far he runs from them. Fortunately, the spirit of the real Saya is able to manifest herself and takes Train out of Doctor's trap, destroying the two fake girls.
Kyoko meets Train while she and Charden are out patrolling for criminals to give the spirit water to. She falls for him, trying to give him one of her popsicles as a thank you for saving her from some thug. She quickly befriends Eve, and Train is shocked to see Charden, who invited him to the Apostle's celebration.
After the Apostles are dismantled, Eve is abducted by Mason, and fused with a machine called Eden. Kyōko calls Charden and the two help to fight against the new Zero Numbers. In the end, their opponents are killed when Eden is destroyed.
In the anime, Kyoko appears to be even more immature and clueless than her manga counterpart. She is also depicted as enjoying her status as a Tao-wielder very much. Despite being part of the Apostles of the Star, she apparently always avoids finishing people off.
Kyoko serves as field agent who assists Charden in breaking many criminals out of jail and providing Shinkito to the most promising of them, under the promise that they would join the Apostles of the Star if their power of Tao is revealed. They come in contact with two failed Tao-wielders, Igor Planter and Gyanza Rujike. Kyoko is still saved by Train from some thugs whom she would have effortlessly defeated and falls in love with him, but this happens in Rubeck City, when she is still part of the Apostles of the Star. She often attempts to kiss him, only for him to use the white stray cat (the series' mascot) as a shield.
Kyoko is seen instead of Charden alongside Maro and Leon when the Chrono Numbers V, VII and XI storm into the ancient castle, but they cannot prevent them from destroying the ceiling and fleeing. She later defects with Charden after Creed kills Durham. Charden tries to remind her that it would be dangerous for her to leave, but she tells him that the only reason she stayed was so that he wouldnt get lonely. Doctor then tries to punish her desertion by shooting her with a nanomachines-infused bullet, in order to transform her into a monster, but Train takes the hit in her place and is turned into a child.
Kyoko eventually returns to Jipang and goes back to her high school, but she sees "Eden" attacking a town in the TV news and manages to catch up with the heroes, the sweepers league and the remaining Chrono Numbers, alongside Charden. Kyoko uses her fire breath to lauch the fireworks needed to distract "Eden," so that the protagonist can invade the aircraft. When the protagonists confront Doctor and the rest of the Zero Numbers, enabling Train and Sven to go further, she offers to go with them but Charden prevents her from following "Mr. Black," stating that her presence is needed here.