It's three years after the events of the original Battle Royale, and Shuya Nanahara is now an internationally-known terrorist determined to bring down the government. His terrorist group, Wild Seven, stages an attack that levels several buildings in Tokyo on Christmas Day, killing 8000 people. In order for the government to study the benefits of "teamwork", the new students work in pairs, with their collars electronically linked so that if one of them is killed, the other dies as well. They must kill Nanahara in three days - or die.

In the future, the Japanese government captures a class of ninth-grade students and forces them to kill each other under the revolutionary "Battle Royale" act.

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