When Megadramon was about to kill Kyubimon, Ryo and Cyberdramon came to her rescue. However, Ryo stopped Cyberdramon from killing Megadramon, as he was not the opponent they were looking for. Rika hated Ryo for beating her in the tournament, and although Kazu and Kenta accepted his offer to reunite them with Takato and the others, Rika declined and left with Kyubimon.
Ryo, Cyberdramon, Kazu, and Kenta met up with Takato and the others in the warped area of the digital world, as Ryo seemed to know his way around. As Ryo led them down a staircase into the desert area, they ended up fighting Majiramon. Ryo used a Goliath card to increase Cyberdramon's size, and after he destroyed Majiramon, he wanted to find another opponent, and left with Ryo.
Later, Ryo and Cyberdramon found Baihumon, the most powerful Sovereign, but decided that the one they must fight, even more powerful than Baihumon, was the D-Reaper. Ryo and Cyberdramon made their way down the pit alongside Rika and Renamon to rescue Calumon, after which they returned to Earth.
After Dobermon gave the tamers and Digimon the power to biomerge on Earth, Ryo biomerged with Cyberdramon into Justimon, who fought against the D-Reaper and its agents, destroying Horn Striker and Paratice Head.
Going into the final battle, Ryo referred to himself as "Digimon King", in response to Rika being known as the Digimon Queen.
During the fight with Cable Reaper, Justimon told Sakuyamon (Rika and Renamon's biomerged form) to transfer her power to him. Rika didn't want to at first, as the force of it could kill him, to which Ryo said that there'd only be one less annoying person to make fun of her, and Rika thought Ryo was trying to impress her, putting aside most of her hatred for him. Eventually Sakuyamon transferred her power to him and he chopped Cable Reaper in half. This was not enough to kill him, but immediately after he was removed by the Sovereign.
Justimon also participated in the battle with Parasimon, after which Ryo attended Rika's birthday party.