Scooby-Doo! 2: Dark Dungeons is the sequel to the Scooby-Doo!: Castle Capers puzzle adventure game and, thus, the game's story continues right after the previous game.

After solving the mystery of the haunted mansion, Scooby-Doo and his pals go deep into the dungeons of the mansion to find the family treasure of the original owner of the mansion, Lady Ebdon.

The starting area acts as a level select area and the place where most of the conversation between the gang and the characters in the dungeons occur. After clearing a level, the next door is unlocked and players can go there. Players can't replay the levels they've already cleared.

In the levels, players have a time limit to find a clue and leave the level through the entrance. Players can switch between Scooby and Shaggy at any time and will need to use both characters to open paths for each other and solve the puzzles of the levels. Although the game has hearts in the top left corner of the screen, both Scooby and Shaggy lose one heart if the enemy touches them and have to start the level from the beginning.