In the Yu-Gi-Oh! manga, Honda is Jonouchi's best friend and fellow bully to Yugi. After Yugi and Jonouchi become friends, Honda still doesn't really warm up to Yugi, until Jonouchi tells Yugi that Honda has a crush on Miho Nosaka, and insists that Yugi can help get her attention. Yugi's grandpa gives Honda a blank puzzle (which Yugi writes a love message on) to give to Miho as a present. Unfortunately, before Miho can open the present and decipher the message, it is discovered by a mean teacher, Ms. Chono, an ugly hag who is as ugly outside as she is inside, but piles on makeup to cover up her true nature.
Yugi punishes her with a "penalty game" and causes the layer of makeup on her face to break up like pieces of a puzzle, exposing how hideous Ms. Chono really is. After the ordeal, Honda asks Miho out, but she turns him down. But after that, Yugi and Honda get along better.
When Jonouchi starts running with his old gang from Rintama high school, Honda confesses that he and Jonouchi were both tough gang bangers in middle school, and that he used to really look up to Jonouchi.
When Yugi and his friends are being put through Kaiba's "Death-T" experience, Honda is trapped and left behind in one of the obstacles. He appears later at the very end, having been rescued by Mokuba.
In Duelist Kingdom, Honda is just there for moral support, though in the anime, he serves as the muscle of the group (though most of the violence is edited out in the dub). While Yugi is dueling Pegasus, Honda and Bakura explore the castle dungeon and get Mokuba's body out of his cell. Honda does this because Mokuba saved his life at "Death-T" and he feels like he owes him.