A dungeon is a generic term in video games generally used to describe an area with hostile encounters, such as caves, forests, ruins, volcanoes, and even literal dungeons. These are usually locations that players need to explore and clear in order to progress through the game.
In Pokémon games, dungeons include places like Viridian Forest, Mt. Moon, Whirl Islands, or even Silph Co. These are all places that cannot be flown out of with Fly and, with the exception of Silph Co., can all be exited from by using an Escape Rope or Dig.
Mystery Dungeons
In the Pokémon Mystery Dungeon spin-off series, Mystery Dungeons are a key part of the game, along with its lore and storyline. These are randomly generated dungeons that consist of many floors—sometimes up to 99 floors!—that the player and their team must clear. Every time you go into a Mystery Dungeon, its items and floor layout on each floor will be different, as they are randomly generated.