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.
- Creepy Cemetery: Not one, but two haunted cemeteries in El Muncho!
- Final Boss: The final boss of the game is Lila's pet alligator Suji.
- Four-Legged Insect: Much like Scooby-Doo! First Frights, spiders only have 6 legs.
- Ghost Town: El Muncho, due to El Scaryachi scaring most of its inhabitants away.
- Giant Spider: Spiders appear in each of the three settings, though are quite rare. The largest of which is found in the swamp.
- 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.
- Killer Teddy Bear: The evil teddy bears from First Frights reappear in the chalet attic.
- Never Smile at a Crocodile: Played with. The game's final boss is Suji, the giant alligator, but after she is fed she is no longer a threat.
- Palette Swap: The arctic wolves have the same character models as the werewolves from the previous game, albeit colored white.
- Pet Monstrosity: Lila's pet giant alligator, Suji.
- 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.
