The Maelstrom was a literal whirlpool in space and time, created when Melanicus stole control of the Event Synthesizer from the Prime Mover. It was considered the "Domain of Melanicus" from where he orchestrated the Millennium Wars.
When the Fifth Doctor and Sir Justin entered the Malestrom at the request of the Matrix Lords, they found themselves in the surreal, dreamlike reality of a demonic carnival, and then later a haunted house. While only seeming to spend a few hours in the Maelstrom, the Doctor discovered upon escaping they had been trapped within for twenty-eight years, allowing the Millennium Wars to rage unchecked.
The Maelstrom ceased to exist when Sir Justin slew Melanicus and the Event Synthesizer was returned to the Prime Mover (who then ensured the Millennium Wars never existed). (COMIC: The Tides of Time)