Digimon Tamers' plot is built around a series of increasingly dark and complex revelations. The initial mystery of 'wild' Digimon appearing in the real world is revealed to be the work of the twelve Devas, servants of the four Digimon Sovereigns. Their goal is to reclaim Calumon, who is secretly the 'Digi-Entelechy,' the living embodiment of digivolution, and whose power they need to defend the Digital World.
A major twist occurs in the Digital World arc with Impmon's character. His resentment and lust for power lead him to make a Faustian bargain with the Sovereigns, allowing him to digivolve to his Mega form, Beelzemon. In a shocking turn, Beelzemon murders Leomon in front of his Tamer, Jeri. This act is the series' point of no return. Takato's subsequent rage is so intense that it triggers a dark digivolution, forcing Guilmon to become the apocalyptic Megidramon. This reveals that the bond between Tamer and Digimon is so strong that the human's negative emotions can corrupt their partner. Takato overcomes this by 'Biomerging' with Guilmon—a literal fusion of their bodies and minds—to become the Mega-level Gallantmon, demonstrating a new, more profound connection is needed to fight the escalating threats.
The ultimate villain is not a Digimon, but the D-Reaper, a primordial data-cleansing program created by humans that has evolved to perceive all life as chaotic information in need of deletion. It captures Jeri, whose deep depression over Leomon's death acts as a perfect nexus of negative energy for it to analyze humanity and fuel its expansion into the real world. The final battle is not just a physical one, but a psychological one to save Jeri from her own despair. The series concludes with the Tamers and their partners being forcibly separated as a consequence of resetting the Digital World. The program that defeats the D-Reaper also recognizes the Digimon as data that doesn't belong in the human world, leading to the heartbreaking farewells. The final scene reveals a portal Takato discovers in Guilmon's old hideout, suggesting a reunion is possible but leaving their ultimate fate ambiguous.