The year is 2071. Following a terrorist bombing, a deadly virus is released on the populace of Mars and the government has issued the largest bounty in history, for the capture of whoever is behind it. The bounty hunter crew of the spaceship Bebop; Spike, Faye, Jet and Ed, take the case with hopes of cashing in the bounty. However, the mystery surrounding the man responsible, Vincent, goes deeper than they ever imagined, and they aren't the only ones hunting him.

After the older DigiDestined are abducted by the mysterious Kokomon, the next generation of kids team up with American DigiDestined Willis to rescue them - only to discover that their enigmatic enemy has an unexpected connection to their new friend!

Six months after the D-Reaper was destroyed, the Tamers are planning to throw Rika a surprise party, but Rika finds out. Suddenly a train-Digimon named Locomon begins to race around the tracks, causing havoc. The Tamers respond to this, as Takato digivolves Guilmon into Growlmon to stop the train Digimon but fails as Takato, Rika and Renamon get on it in an attempt to slow it down. The others, excluding Suzie, use a freight train to catch up with Locomon

Omnimon confronts Mephistomon (who was formed from Apocalymon's data) in a dark corner of the Digital World over Mephistomon's attempt to destroy both the Digital World and the Real World and incorporate the data in order to become truly invincible. They fight, but then Mephistomon sees a chance and slips into the Real World.