Gyro, Fenton and Huey take a malfunctioning B.O.Y.D. back to the lab where he was created in Japan, but as Huey bonds with the robot boy, a secret from Gyro’s past threatens to destroy the city and Gizmoduck.
At a Junior Woodchucks camp out, Huey is mocked by Bully Beagle and several other campers for his strict adherence to procedure. He then meets and befriends B.O.Y.D., who shares his enthusiasm for rules. Unfortunately, B.O.Y.D. begins firing laser beams from his eyes, much to the shock of Huey who is unfamiliar with the android child. Seeking help, he takes B.O.Y.D. to the Money Bin, where Fenton Crackshell-Cabrera is quick to take the pair to see Gyro Gearloose.
Gyro not only provides a means of stopping B.O.Y.D.'s lasers, but recognizes the robot as one of his own earlier creations. Lacking the tools to work on B.O.Y.D., he reluctantly decides that their only option is to travel to Tokyolk, Japan, where B.O.Y.D. was built. He also insists that Fenton bring along the Gizmoduck armor, regarding B.O.Y.D.-or 2BO, as he was originally known-as a dangerous threat. Gyro's word is apparently verified when, shortly after arriving in Tokyolk, the group is confronted by Inspector Tezuka, who blames Gyro and his mentor Akita for an attack on the city twenty years earlier.
After Tezuka is lured away by Lil Bulb's misbehavior, Gyro leads the group to his old lab, which has been boarded up. Hooking B.O.Y.D. up to a diagnostic computer, he leaves to look for a replacement part for Lil Bulb. After seeing some of B.O.Y.D.'s memories, including his time with Doofus Drake and discovery and naming by Mark Beaks, the group overhears a police report of a break-in. Fenton, believing that B.O.Y.D. would make an ideal sidekick for him, dons his Gizmoduck suit and takes off.
Unbeknownst to the group, their intrusion has not gone unnoticed, with Dr. Akita observing their departure from a hidden lair. Huey and B.O.Y.D. become separated from Gizmoduck after trying to arrest two thieves, but at B.O.Y.D.'s urging spend an enjoyable day exploring the city together. Meanwhile, Fenton runs into Tezuka again, and after being subdued by her learns that B.O.Y.D. attacked the city twenty years ago. Unaware of this, Huey comes to the conclusion that, despite his robotic nature, B.O.Y.D. is a child at heart.
He is further convinced when B.O.Y.D. saves him from an otherwise fatal fall, only for Akita to be alerted to the robot's presence. He then emerges from his lair, while at the same time Huey and B.O.Y.D. meet up with Tezuka and Fenton. Gyro then appears and refutes Huey's claims, and reveals the truth behind what happened twenty years ago. B.O.Y.D., then known as 2BO, went on a rampage that Tezuka was forced to stop, and leaving Gyro guilt-ridden ever since.
Gyro then reveals that his intent is not to repair B.O.Y.D., but to shut him down permanently, believing him to be a threat to the world. B.O.Y.D., who begins acting strangely, flies off, and turns out to have been summoned by Akita. The lunatic doctor unleashes him upon Tokyolk, and Fenton desperately tries to stop him as Gizmoduck. Upon examining B.O.Y.D.'s memories from his diagnostic, however, Huey learns that Gyro programmed B.O.Y.D. to mimic a real boy. However, Akita-who was as demeaning towards Gyro as he is towards Fenton-purposefully inserted his own programming to turn B.O.Y.D. into a weapon.
As Gizmoduck and Tezuka continue their desperate struggle against B.O.Y.D., Gyro and Lil Bulb engage Akita, and manage to knock him out. B.O.Y.D., defeating his attackers, then zeroes in on Gyro, who admits his realization that B.O.Y.D. isn't merely a robotic weapon. His admission allows B.O.Y.D. to override Akita's programming, and android and creator embrace. Huey, reunited with B.O.Y.D., encourages him to choose his own name; the robot decides to retain his current acronym, but changes its meaning to "Be Only Yourself Dude."
With Akita apprehended, Gyro admits that he was wrong to treat Fenton as he had previously, and hires him on as a full-time employee. Overjoyed-though not so much that he fails to point out Gyro's error in addressing him as "Dr." Crackshell-Cabrera, Fenton embraces his employer, much to Gyro's chagrin. Feeling victorious, the group anticipates exploring Japan further, but Tezuka demands that they leave immediately. As such, Fenton and B.O.Y.D. fly their companions home, though B.O.Y.D. decides to perform some aerial acrobatics on the way.