During the summer of 2000, Ryo was visiting with Ken, and they witnessed Taichi's and Yamato's battle against Diablomon. Ryo panics, and sends a good-luck email, and is happy when Diablomon is defeated by Omegamon. Suddenly, V-mon appears and tell Ryo his help is needed again, and a blue colored D-3 appears. Ken and Ryo go to the Digital World.
(Although many cite the reason for the games being out of continuity as being that Ryo was far from Ken's house during Our War Game, it is concievable that he saw the battle from there, and then went to Ken's house. Also, the D-3 and V-mon eventually become Daisuke's, and this was the point when Ken became a Chosen Child.)
Once he has arrived in the Digital World, Ryo and Ken find Agumon, Taichi, Gennai, Piccolomon, and others waiting for them. Gennai explains that a remnant of Diablomon escaped, and went to a nearby mountain. Ryo and V-mon leave for the mountain, where they encounter Diablomon. Diablomon is easily defeated by V-mon, when Millenniumon appears, laughing, and saying everyone fell for his trap. Ryo has returned to the Digital World, and now he can get his revenge. He then creates a massive explosion that rips the Digital World in two, seperating Ryo and Ken, turning Taichi and Agumon into stone, and knocked Gennai unconscious.
Ken soon meets up with Wormon, and Piccolomon and Gennai set up a machine that can communicate and transfer items between the two halves of the Digital World. Both Ken and Ryo then begin chipping away at Millenniumon's power, by defeating his underlings. They also find pieces of the Digimentals, which they are able to rebuild.
There are many more Digimentals in the games than there is in the card game and anime. Not all are used to evolve; some give a Digimon special powers or a new attack.
Eventually, the Digital World is reformed, and Ryo and Ken take on Millenniumon. He is once again defeated, and with his last moments he shoots out a Dark Spore, aimed at Ryo. However, Ken pushes Ryo out of the way, and takes the Dark Spore in his neck. Ryo then seals what remains of Millenniumon into a crystal, which later becomes Moon=Millenniumon. Ryo and Ken return to the human world.