D-reaper

The D-reaper was a program that was not a Digimon, nor anything from the Real World.

Instead, it was a horrible creature bent on destroying everything, with no remorse for it's actions. It seems to be sentient, as the Mother-form speaks to the Digidestined in the end of Arc 5.

Past
The D-reaper existed long ago, and did battle with many digimon, destroying almost all of them. It wasn't until the Oracle of the Digital World, Gennai, sealed it underneath the Digital World, that peace returned.

Between Arcs 2 and 4
After the Digidestined left the Digital World, there was nobody to protect it. Slowly, it broke free from it's underground prison, and took over the digital world, reformatting it and destroying it. Gennai fought with it, but was eventually defeated.

Arc 4
At the start of Arc 4, The D-reaper breaks through the barrier between the worlds and sends seeds around the world to spread and take over. However, the digidestined manage to destroy them one by one.

By the time the Digidestined return to Kyoto, the D-reaper had spread and taken over the entire city. Eventually, Neroe defeated the core that spread through Kyoto, and it returned to the digital world.

Arc 5
By the time of Arc 5, the D-reaper had completely rearranged the Digital World. It was now a bunch of floating zones, rather than a coherent mass of continents. It had turned its prison into a fortified base, protected by a barrier powered by towers spread around the digital world.

The Digidestined travelled around the digital world destroying these towers, which eventually broke the barrier, and allowed them to enter the D-reaper's base and destroy it.

During Arc 5, the D-reaper was revealed to have a new ability; it could spread it's tentacles into digimon and control them. Alphamon was the only digimon not known to be controlled this way, and willingly worked for the D-reaper.