The story of Monty Python's Invasion from the Planet Skyron follows the Lost Boys as they navigate through nine levels to figure out what actions to take. Along the way, they encounter various sketches and elements that may lead to positive or negative outcomes. A sheep accompanies the group, keeping track of their score, which increases or decreases depending on their actions.
The gameplay involves guiding the Lost Boys through each level, interacting with the environment by clicking on elements. The outcome of these interactions can be unpredictable, adding a sense of uncertainty to the experience. The game features several mini-games, including memory tests and "guess who said it" games, which offer additional scoring opportunities.