How Ken Became The Digimon Emperor.

The story started off with Ryo visiting Ken Ichijouji in his room. They witnessed Diaboromon's defeat by Omnimon on the Internet, and Veemon (at a later point in time to be Davis's Veemon) appeared from the computer with a D-3 for Ryo. There was an extra Diaboromon loose in the Digital World, and Ryo was called in to defeat it. Ken followed along, only to be left behind in Primary Village with Taichi and Agumon to wait for Ryo's return. The Diaboromon, hiding out where Devimon used as his base, was easily defeated with just Veemon's strength. Millenniumon showed up soon after to reveal that he was waiting for Ryo and that the Diaboromon was simply a lure used to draw Ryo back into the Digital World. He blew up the mountain, and in doing so, ripped the Digital World into two. From then on, the story's point of view switched between Ryo and Ken. Ken woke up in a forest clearing to meet his digimon partner, Wormmon. Ken searched for Ryo at first, but Wormmon took him to Gennai, who told him that Ryo was on the other half of the world. During this, Gennai said that they must set up a mirror site, and that Ken is a Chosen Child. But he doesn't want to be a Chosen Child, Ken says. Only after Wormmon guilt-tripped him did Ken accept. Ken was then told to clear out the beach side of the continent, where he picked up the pieces of Digi-Eggs, cleared several dungeons taking the form of a ziggurat, an Egyptian pyramid, a Mayan pyramid, and a Black Ship. Once he returned from his mission, Gennai and Piximon set up a Reload Machine that would allow Ryo and Ken to contact each other and share items. The scene switched to Ryo, who must follow on Ken's path and jump ahead to another dungeon to clear. Thus the name, Tag Tamers.

After many battles, DNA Digivolutions, and archaeological digs for more Digi-Egg pieces, Ryo eventually arrived at Millenniumon's floating continent. Millenniumon, speaking in archaic Japanese, chuckled and said that he could not be defeated by just one power. The key to his power cannot be unraveled, and the door will never be opened. He then disappeared, and a single locked door turned up outside of Primary Village. Back at base, Piximon said that Millenniumon still had several traps on Ken's side of the world, so the scene switched to Ken.

Along the route to Millenniumon's dungeon, an Elecmon told Ken that the locked door led to Millenniumon's heart, then wonders if Millenniumon has a heart at all. In a sharp contrast to his more polite interaction with Ryo, Millenniumon was outright rude to Ken and insulted him before disappearing.

The key to the locked door was the completed Digi-Egg of Desire, which only reacted to Ryo. Once it opened, Ryo, Ken, and their digimon were absorbed in darkness and taken to Millenniumon's world: a barren wasteland with a gigantic metallic sphere hovering over it. The sphere was Millenniumon's castle. Millenniumon welcomed Ryo warmly to the world created from his mind. To Ken, his voice dropped coldly as he said that everything that happened there happened also within him. Ken's power is limited there. Then he turned again to Ryo, chuckled, and invited them to challenge him, even though they trembled in despair.

The battle that ensued destroyed Millenniumon's body, even as he laughed in his defeat. With Millenniumon's defeat, the Digital World, Taichi and Agumon returned to their normal states. Then Millenniumon returned only to disperse his Dark Spores. Ken shoved Ryo out of the way of one, only to get it in Ryo's stead. Millenniumon's spirit chuckled. He can never die, he said, and as Ryo's power is eternal, so is his. He then disappeared.

In the scene afterwards, Wormmon said that Ken became sick and increasingly cold to him. The epilogue was meant to show Ken's eventual fall into the Kaiser persona a year later, and in it Ken said that he was different from Millenniumon. He was the Digimon Emperor.