The Chosen Children are stunned by Meicoomon"s betrayal, the digital creature that had recently joined their ranks together with her human ally, Meiko Mochizuki. Koushirou Izumi is set on diagnosing the illness that has seized control of Meicoomon. At the same time, Takeru Takaishi notices that his own partner, Patamon, is beginning to show frightening signs akin to those seen in other infected Digimon such as Meicoomon.
Suddenly, the Chosen Children receive a communiqué from the enigmatic force Homeostasis, warning them that their world faces imminent annihilation—and so does the Digital World, the Digimon"s homeland. Homeostasis intends to trigger a "Reboot," which will overwrite all data that composes the Digital World and wipe out the infection. Yet this Reboot would also erase every Digimon"s memories, including those of the Children"s partners. Will the Chosen Children halt Meicoomon before the Reboot becomes unavoidable, or will this mark the end of their in this shared journey for their beloved Digimon?