A few days after the events in Tag Tamers, Ken was still sick in bed and being nursed by Ryo. Ken pointed Ryo to his computer, saying that there was something Ryo should see on it, and Ryo found a page leading to a quiz for potential participants in something called the D-1 Tournament. Curious, Ryo began answering it. With each question, it became increasingly clear that the quiz was rigged in such a way that he would be the only one to know all the answers. He then turned to Ken asking what that was about, but Ken had no idea. As no real answer was forthcoming, Ryo went on to finish up the quiz. Once one of the four Harmonious Ones (Holy Beast) was chosen, the shadow of that particular Harmonious One abducted him from Ken's room in the real world.
Ryo was then dropped off in the Digital World and told by Piximon that they need Ryo's power again. Understandably skeptical, as he was only called to the Digital World when Millenniumon was on the rampage, he asked why. The Harmonious Ones that ruled over the Digital World called a tournament, Piximon replied. Gennai added that other children were called in to participate and urged Ryo to go to the arena.
Once there, a group of tamers gathered around to bully Ryo. One said that he expected better of someone who defeated Millenniumon. Another asked whether Ryo can remain undefeated. Unwilling to stand up for himself, Ryo said nothing as the other tamers closed in. Before a brawl could commence, Piximon appeared to break it up, said that the tournament was to find the greatest tamer and that they should all get along better than this, and sent Ryo back to Gennai. At Gennai's house, Ken greeted him from Gennai's monitor. Gennai set it up so that Ken could still communicate with Ryo through the computer and D-Terminal, since Ken was still sick and thus stuck in the real world. ToyAgumon turned up just then to announce that the Harmonious Ones would address them all.
The Holy Beast introduced himself (as the one the player chose during the quiz) and explained that the other three Harmonious Ones became evil and were preparing to defeat the good one, before going on to their individual plots to eliminate each other so that only one could rule the Digital World. The child that would win the tournament would be declared the strongest and chosen to partner up with that Holy Beast to bring his brethren to their senses. Piccolomon then explained the tournament and that it was in five stages. The competitors were to train before tackling each stage. After Wormmon, Agumon, and Veemon offered their aid, Ryo trained and went on through each stage and dungeon that opened afterwards. Grade 5 was headed by Izzy Izumi, Grade 4 by Willis, Grade 3 by Mimi Tachikawa (who asked Ryo to go out with her on a date after the tournament was over), Grade 2 by Matt Ishida, and Grade 1 by Tai Kamiya. Ken offered advice and suggestions through the D-Terminal.
For the first three stages, nothing really eventful happened. It's afterwards that things went along a downward spiral: the Digimon Graveyard dungeon required Ryo to sacrifice a digimon so he could escape. After Ryo won the final grade, Taichi revealed that although neither of them knew it originally, the D-1 Tournament was a hoax. Ryo had already been selected to win anyway, it was all training so that Ryo would be strong enough to take on Moon-Millenniumon, the bodiless spirit form of Millenniumon, and no one else could defeat the crystal moon beast of death. Even as the other Chosen Children apologized for deceiving him, Ryo remained silent and closed off against them. He would remain this way for the rest of D-1 Tamers and into Brave Tamer. Nonetheless, Ryo marches on through the final practice dungeon before being sent to Moon-Millenniumon's floating island.
This time, Millenniumon's lair is in a crystal tower on the floating island. Moon-Millenniumon said that he had been waiting for Ryo, he had revived to challenge Ryo again, and no Digimon is a threat to him anymore. Not even the Holy Beasts can defeat him. But Ryo is different, he said, for Ryo is the only random element that makes the impossible possible. After his defeat, Moon-Millenniumon reveals that he and Ryo are Yin and Yang, that one cannot die without the other. If he was defeated, so was Ryo. He invited Ryo to fly with him through the worlds of time, and the floating island exploded.
From that point on, Ryo was considered dead in the Digimon Adventure universe. Despite constant searches, he was never found and everyone but Ken gave up hope.