The plot involves Mandark taking over control of Dexter's lab. Dexter has to find a way to regain control of his laboratory.
Dexter's Laboratory: Mandark's Lab? consists of a series of mini-games based off of various episodes of the cartoon. The mini games feature various genres, such as first-person shooter and racing. Outside of the mini-games, Dexter walks around a 3D version of his house and laboratory looking for objectives.
This game provides examples of:
- Dance Off: The first mini-game is a rhythm game that involves Dexter and Dee Dee having a dance off.
- Expressive Hair: Dee Dee's pigtail curve downwards when she loses in the first mini game.
- Girls Have Cooties: Dexter must venture into Dee Dee's room. It's filled with cooties, so the player must first go through a first-person mini-game where he sprays the cooties dead.
- Racing Minigame: One of the minigames is based off of the episode "Mock 5". In it, Dexter must win a soap box derby.