In 2071, roughly fifty years after an accident with a hyperspace gateway made the Earth almost uninhabitable, humanity has colonized most of the rocky planets and moons of the Solar System. Amid a rising crime rate, the Inter Solar System Police (ISSP) set up a legalized contract system, in which registered bounty hunters, also referred to as "Cowboys", chase criminals and bring them in alive in return for a reward.

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.

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.

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!

Takato, Ruki, and Lee are children who have, by fate, received real Digimon, unlike the imaginary ones in the card game they play. Each of the children, or Digimon Tamers, have their different views on how Digimon should be treated. But when other Digimon begin to appear around Japan, they must put aside their differences to fend off the digital intruders.

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