The fortress only has a chance to generate the prison room if at least three Withers have been slain, but it doesn't matter if this is in the Nether or Overworld (or the End). The Nether Dragon is initially found imprisoned in a Nether Fortress, in an impenetrable bedrock prison. The Nether Dragon is a Serpentine-Cuboid Dragon and boss mob which can be found in the Nether.