The only real villains in Tamers was the D-Reaper and it's agents, so that's all that will be listed here.
The D-Reaper had once attacked the Digital World in the past, but left. But it returned again, sensing that Digimon were exceeding their boundaries. The D-Reaper made it to the Real World as well, and while the Holy Beasts used the Shining Evolution to evolve all Digimon to Final, they sent a Dobermon that would allow the Tamers to Matrix Evolve in the Real World to combat the D-Reaper there. Although relatively few casualties seem to have been sustained in the Digital World, the Tamers were having trouble against the D-Reaper, as they only had four Final levels. They combated countless Agents, and with the aid of a Red Card provided by Shibumi they were able to enter the D-Reaper Zone itself. There, they met the Shinigami Reaper, ADR-01, and the Mother D-Reaper. ADR-01 had been posing as Juri, whereas the Mother D-Reaper had summoned the Shinigami Reaper from the Digital World to help it in the Real World. Sakuyamon and Justimon sliced the Shinigami Reaper in half, but it regenerated. However, the Holy Beasts were able to push it back to the Digital World, where it was later devolved. ADR-01 nearly killed Dukemon Crimson Mode, but a furious Guilmon and Takato retaliated with a devastating punch that killed it. Mother D-Reaper was sucked into the Shaggai vortex.