Spygirl works for M.A.N.G.A. (Middle Asian Network for Global Activities), the sister organization for US covert agency S.H.I.R.T and is the star of her own TV Series. She first encounters Spyboy when the plan they are traveling in has to make an emergency landing. She greets Spyboy and then comes face to face with a very angry Bombshell. The two have a history that is not explained immediately. The two begin fighting with an unfortunate Alex Fleming caught between the two hellcats (and he seems to get the worst of their scuffle).
When the fight is broken up the group is taken to a M.A.N.G.A.base and it is revealed that during a joint M.A.N.G.A./S.H.I.R.T. operation Spygirl opted to take the decoding device that Bombshell had acquired and cut her losses leaving Bombshell to suffer at the hands of her captors. This act of betrayal sours Bombshell to working with anyone and she feels she can't trust anyone but herself (trust was already an issue as Bombshell was abandoned by her parents). Spygirl further gets on Bombshell's nerves by first, revealing that her real name is Phylis and second, by kissing Alex.
The team of Spyboy, Spygirl & Bombshell are dispatched to stop the villain, Annie Mae, a villain that is responsible for the death of Alex's Mother & crippling his grandfather. The team witness Slackjaw leaving in a giant mecha dragon known as Killadilla. The group find Annie Mae and convince her to give them the means to stop Slackjaw, The Iron Giant Chef. After a huge battle the Spy Team defeats Killadilla, smashes Slackjaw and throws in in the ocean.
After leaving Japan; Alex, Bombshell, and Butch are all suprised to see that Yukio is now assigned to asses Alex's abilities (which is ok since her TV Series is on break for the summer). She wears a blonde wig to hide her pink hair and is under the alias of Kimmy. She helps Alex win class president and saves him from an assassin hired to kill him.
In Young Spies Like Us (Young Justice/Spyboy Crossover) Annie Mae sends SD's to attack S.H.I.R.T. and A.P.E.S. (DCU - All Purpose Enforcement Squad) to get the two groups of heroes to fight one another. The plot is hatched by Harm who has Rip Roar as his muscle to deal with Slackjaw should he be a problem. After a classic heroes vs heroes fight the two groups manage to figure out they've been had and find the real villains. It is heavily implied that Tim Drake (Robin) and Yukio are attracted to one another.
In Spyboy: Final Exam Yukio is present to save Spyboy's life (though he claimed he was in the process of figure out how to save himself) after he's blown out a window. When the group returns from the mission Alex is rather upset that one of the ladies of his affection, Lori, has a date with another guy. When Yukio as Kimmy inquires what is wrong Alex asks her to the prom. She comes off not to understand why until Alex sreams using several words that are bleep out (to the readers) if she wants to go with him just to go. Yukio kisses him and accepts.
At the dance Alex spends some time watching Lori dance with her date and Yukio brings this to his attention. He appologizes and begins to compliment her on her beauty when suddenly he is arrested as a Teen Terrorist. Bombshell is nabbed as she pulls out a smoke grenade and Yukio manages to get the device to activate Spyboy and does just that. Alex escapes while the rest of the crew and Alex's dad are arrested.
The group is broken out by Butch's mother, who in reality is Alex's long thought dead mother Anita, and as they drive off Sean Fleeming reveals to the group that Anita is his wife, not Butch's mom. Anita reveals the truth to everyone and after a truce is called they go to meet with Spyboy who is unable to decide what to do next.