Shaggy and Scooby are asked by a mysterious swamp witch named Lila to find ingredients for her while helping their friends solve mysteries.
This game provides examples of the following tropes:
- Bigfoot, Sasquatch and Yeti: The second mission features a giant yeti that turns out to be an animatronic disguise.
- Continuity Nod: During the second mission, Daphne mentions dealing with the Phantom the last time they met her cousin Anna, a callback to Episode 1 of First Frights.
- Final Boss: The final boss of the game is Lila's pet crocodile Suji.
- Good All Along: Lila gives the impression of manipulating Scooby and Shaggy, but in the end it turns out that she just needed help making food for her pet crocodile Suji.
- Identical Twin ID Tag: The first mission has twins Emilio and Esteban. They wear clothing that mirror each other, plus Esteban has a blue belt while Emilio wears an orange belt in addition to having facial hair.
- The Voice: Anna's boss Sergio is only heard speaking, being too cowardly to exit the basement door after Shaggy and Scooby run the errands he asks them to.
- Wide Open Sandbox: Unlike its predecessor, First Frights, Spooky Swamp features three different open worlds that can be revisited after completing the game.