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Yugi's friends Miho and Warashibe are obsessed with Capsule Monster Chess. After Miho spurns his advances, Warashibe decides to eliminate his competition for her affection. This leads to him challenging Yugi Mutoto a game of Capsule Monsters.
The group soon finds out about the Capsule Monster Chess game (Capmon for short) when Miho obtains a Gacha Box (a capsule container) whose capsules are filled with jewelry of Miho's fancy. Miho then reveals it was Warashibe, a college student whom she met just recently, that sent it as a present to her. While Yugi briefly explains Capmon to others, Miho expresses her joy of the present, much to Honda's protest.
Soon after, Yugi meets up with Warashibe, with whom he has been a friend for some time now due to their common interest in Capmon (a "Capmon buddy" as Warashibe calls it), and informs him on Miho's reaction on the present (the whole thing revealed to be Yugi's idea in the first place). Warashibe reveals his obsession for Miho, explaining how he saw her briefly through a show window while obtaining new Capmon capsules. Ever since, Warashibe has been convinced the two were fated to be together, and keeps referring to Miho as his "Capmon Goddess", and he is dedicated to win her heart, much to Yugi's dislike of his extreme reaction.
Later that evening, Miho visits Yugi's grandfather's shop and obtains a minor Capmon capsule, intending to send it to Warashibe as a token of graditude for the present, thinking of Warashibe as a pen-pal. However, Warashibe misinterprets the message as a love confession, and leads Yugi to his secret base filled with rare level 4 and 5 Capmons on the next day. He asks Yugi for his help in order to meet Miho in the most romantic way he can imagine, but Yugi, initially shocked by the idea, tries to refuse, yet Warashibe's babycry soon convinces him otherwise.
Yugi and Warashibe then try executing the plan for him to meet Miho (which consisted of Yugi putting on a ridiculous disguise and pretending to be assaulting Miho, and Warashibe "saving" her), which fails miserably not only because Miho sees through Yugi's disguise, but also repeatedly strikes Warashibe with her purse as he was being too direct to her in his confession. Miho runs away crying out loud how she doesn't know anything about Capmon, leaving Warashibe beaten and heartbroken. Due to the rejection, he later mayhems his base and ponders what he did wrong, eventually concluding there must be a reason why she refused him, and sets out to eliminate it.
On the next day, Warashibe disguises himself as a member of the kitchen staff in Domino High cafeteria, and after concluding Miho rejected him because Jonouchi, Honda and Anzu were in the way, decides to eliminate them by offering them glasses with poisoned water. As a result, all three end up hospitalized in the nursery with a bad stomachache, with only Yugi and Miho remaining healthy. Miho then receives a letter from Warashibe, who claims to have brought judgment upon those who interfeere with their fate. This makes Miho truly angry (for the first time in the series), and she immediatelly asks Yugi to lead her to Warashibe's place.
Once there, the enraged Miho scolds Warashibe for what he did, for what he shows no remorse. After being rejected for the second time, Warashibe proposes they settle the argument with a game of Capsule Monsters, with the stakes being that Warashibe would leave Miho alone if he looses, but Miho will have to accept her fate as his sweetheart otherwise. The angry Miho accepts.
At the start of the game, both Miho and Warashibe take turns in taking out their respective capsules from a capsule machine, and while Miho ends up with a bad set (3 level 1, and one of each level 2 and 4), Warashibe's set of capsules contains only high level monsters (a total of 3 level 4 and 2 level 5 monsters). Despite claiming to have studied the rules of Capmon, Miho ends up pushed in a corner and Warashibe easily takes out one of her monsters on the first turn.
Angry with the resluting table, Miho yells at Warashibe and accidentally pushes Yugi into the capsule suspensor, which tips over and breaks, revealing a hidden device that Warashibe installed previously in order to rapidly exchange low and high level Capmons, thus resulting in Miho getting only weak monsters, and Warashibe the strong ones.
Realizing that Warashibe cheated using a rigged machine, Miho declares herself winner and tries to leave with Yugi, but both are stopped by Warashibe's dropping bars that blocked the exit. However, the mechanism malfunctions and instead results in a large beam dropped atop of Miho and Yugi. As the dust settles, much to Warashibe's surprise, Dark Yugi emerges with Miho in his arms, then challenges Warashibe to a Shadow Game.
Dark Yugi agrees to continue with Miho's current set field and set of monsters, which Warashibe reluctantly agrees on, and is impressed how the Shadow Game made the monster figures come to life, and one of each of their monsters already anihilated each other. Warashibe then destroys another one of Yugi's monsters with Dinosaur Wing, and after Yugi makes a turn by placing his next monster without attacking, Warashibe destroys it with Head Sucker, leaving Yugi with only one monster left.
Claiming to have won the match, Warashibe is then asked to look at the field, and he realizes all his monsters were alligned in a diagonal pattern, which is what Yugi was counting on. His last remaining monster is Torigun, who despite his otherwise low rank and limited battle qualities, posesses a special skill that goes in Yugi's favor: it can move and attack in a diagonal pattern, and destroy any monster it comes across, even if it's a level 5. With this move, Toribe destroys all of Warashibe's remaining four monsters, winning Yugi the game.
Warashibe is shocked by the outcome, with Dark Yugi telling him how Capmon is not something to be collected, but played with, and know how to win using every monster's ability. Warashibe becomes struck with rage, and after flipping the table in frenzy, he still demands Miho to become his, for which Dark Yugi inflicts a Penalty Game on him, capturing him inside a massive monster capsule (whether or not this was just an illusion or an actual mental punishment was not shown) before leaving with Miho.
With Jonuichi and others recovered, they discuss how it is better now with Warashibe off the scene. As Jonuichi complains that he never wants to hear about Capmon again, a cheerful Miho comes running. She trips and falls, revealing her purse was full of Capmon capsules.