The Dark Whirlpool is a whirlpool in the ocean within the Digital World, which is said to be a portal to other dimensions and a conduit of dark energy. Much of its nature is not revealed, except that it was caused by the spirit of Devimon, after Angemon destroyed him.
It appeared while the Digimon Emperor was searching for it to complete Kimeramon. He sent some Mekanorimon after Devimon, but they were sucked into the whirlpool, so the Digimon Emperor got into a Mekanorimon and sucked Devimon in, absorbing him into Kimeramon, despite Devimon's warnings that he could not control the powers of darkness.
Any Digimon near the Dark Whirlpool would feel the presence of evil. The whirlpool is full of evil spirits. It is also believed to be a portal to the "dark area", possibly where evil Digimon go when they are destroyed, hence Devimon's appearance there. It is unknown how often it appears or whether this was the first time, but if it was caused by Devimon as the Digimon Emperor believed, it presumably disappeared once he was re-killed along with Kimeramon.