Makoto first appears as she attempts to send a dummy Navi into a Copyroid, however several warning signals pop up, and the Copyroid falls to the ground. She suspects the energy conversion program to the problem, and ponders on a solution before receiving a mysterious e-mail with a code to another energy conversion program. She visits Meijin at the SciLab, who is surprised to see her. Netto Hikari asks who she is, and she reveals herself to be Meijin’s ex-girlfriend, much to his embarrassment as his coworkers, Netto, and Meiru Sakurai all grin at him. He introduces her as the daughter of his old teacher and a brilliant scientist. He asks why she is here, and she asks for his help finding the combination in the energy conversion program that outputs the most energy. They talk of his love of puzzles as Netto and Meiru as well his coworkers attempt to eavesdrop.
He tries several combinations, and while looking the two pull the paper of code two different ways and rip it as they exchange glances. Later, when Netto has brought them some food, Meijin gazes at Makoto and blushes before asking her how the Copyroid project is going. The two share things they know about each other before a combination that outputs enough energy is found. Meijin asks if Makoto really made the program, but she quickly downloads and it leaves stating she’ll take him to lunch some time.
Back at her lab, she installs the energy conversion program, which is successful, though while she checks for abnormalities, she is watched by Zoano Punk.EXE, who enters the Copyroid when she attempts to plug the dummy Navi in and captures her. He takes her away and throws her down on a rooftop before causing mass destruction as she watches. He then brings her back and talks to her in Beyondard language before downloading Earth’s language and demanding Makoto make more Copyroids, revealing the Zoanoroids are the ones who sent her the energy conversion program and he will not take “no” for an answer. After finishing dozens, Zoano Punk intimidates her with his Punk Chain attack and wants to know why she’s taking so long to power them. She states Copyroids are meant to bring humans and NetNavis together, and Punk tells her if she does not do as he says he will destroy the university she works at, and she reluctantly uses the energy conversion program to power the Copyroids.
Later as the Copyroids are loaded into a semi-truck, Punk thanks her for helping Falzer’s army, and she tells him her Copyroid research wasn’t meant for war. Punk tells her to not be mistaken: she may have handled the Copyroid research, but the energy conversion program which completed them was made by the Zoanoroids. As her work was complete, he attacks her, though Meijin saves her and the two flee from Punk. He cuts the two off, but C.F. Rockman and C.F. Blues arrive and combat Punk, who uses his Shield and Chain attack and destroys Makoto’s Copyroid data as she watches in distress.
After Punk is defeated, she watches as the semi full of Copyroids drives away and falls to her knees, grief stricken over what she had just done. Netto comforts her, and states her intentions for the Copyroids weren’t wrong, the Zoanoroids are. She thanks him. Copyroid (episode)
Makoto later develops the Hyper-Magnetron to utilize the Copyroid's weakness. As she and Meijin fly to the Firewall Research Facility in a helicopter, she explains the defect lies in the energy core, where unprocessed energy is located. The unprocessed energy is used to prevent the energy conversion program from becoming unstable. The Magnetron's purpose is to provide electromagnetic pulses to the core, which will cause the Copyroid to self-destruct. She thanks Meijin for helping her and leans against him, saying she knew she always needed him, causing him to blush swerve the helicopter. A pod containing Copyroids from Glaga’s army blasts past them and crashes into the Research Facility, and Zoano DarkMan.EXE plugs into one of the Copyroids. Dr. Hikari has the Ministry of Science activate a Dimensional Area that Meijin barely enters and the two crash land before rushing into the facility and testing the weapon against a substantiated Zoano GutsMan.EXE, who was using a Copyroid. He is deleted and Raika attempts to use it against Zoano DarkMan.EXE, who escapes through a Fossa Ambience before the Copyroid was destroyed. She watches on as Netto, Enzan, Raika, Meiru, and Dingo are sucked into the Fossa Ambience and taken to Beyondard. Synchronizer (episode)
She is present as Dr. Hikari attempts to get in contact with those who were sucked into Beyondard in vein. As Dr. Hikari explains the only way he can think of to get a hold of them is through a device DarkMan left behind, Meijin and Makoto offer to help. The three take apart DarkMan's device and learn its an activation device that sends a signal to a main receiver in Beyondard, which in turns opens a Fossa Ambience on Earth. Beyondard 2