Mokuba saw Yugi for the first time after the Beauty Contest ended while Yugi was walking the way home and he was passing in his limousine fingering character eggs from Capsule Monster Chess in his hands.
He was reunited with his brother at his office to discuss about their rival, Omega Town and he was with Daimon during the duel to obtain some CD's with game secrets. He also greets his father Gozaburo when he landed with his helicopter.
After Daimon's defeat he helped Seto to prepare the Death-T for his revenge against Yugi. When Yugi and co went with Bakura to the new Game Center, they discovered that Mokuba was in the first place of the ranking list (his alias is KAI), and that he is a top gamer in all the games of Japan. When the gang were playing a car game competition (Wild Racing) Mokuba appeared in a limousine and threw a bomb to stop the game. Then, Mokuba and Seto used the game to inform Yugi about his Grandpa being kidnapped by them and his invitation to Kaibaland to participate in the Death-T.
Mokuba was beside Seto watching Yugi and co fighting in the first three stages. Later, he talked with his brother about a bet they made before the Death-T plan was finished, about in which stage they will defeat Yugi. Mokuba bet Death-T4 where he will fight Yugi, but Seto bet Death-T5 and Mokuba was angry because Seto didn't believe in his own brother. Seto tells him that in the world of games, there's no such things as "brothership" and until he don't understand that he can't defeat Yugi. Mokuba went to the stage sure to defeat Yugi and demonstrate Seto he was wrong.
Mokuba challenged Yugi to a Capsule Monster Chess duel inside a battle box. He tricked Yugi by playing with higher level monsters than the ones played by Yugi. Although Mokuba had a great advantage, he lost against Yugi's strategy. Then, Seto decided to punish him with a virtual Penalty Game. However, Yugi saved Mokuba by taking him out of the battle box. When Mokuba asked Yugi why he save him; Yugi's answer is that he holds his rival's hand the same as his friends hold his own hands, that's why he won the game.
Yugi's attitude reminded Mokuba of his past life with his brother and how kind he used to be, hoping that Yugi will be able to help him. After Yugi defeated Seto, he used the Mind Crush to pierce his evil heart, Mokuba stayed with him and decided to wait until he came back.