The game is presented from a two-dimensional side view. Bart travels through several Springfield-themed stages, each built around a different alien objective and a specific task that must be completed before the level ends.

Bart can jump, move around platforms, use stage items, and activate his x-ray vision to identify disguised aliens or useful targets. Progress depends more on solving environmental problems and finding the correct targets than on simply reaching the end of a course.

The stages include tasks such as removing alien-colored objects, exposing aliens, and dealing with crowds or hazards. Completing a stage advances Bart to the next plan, while limited lives and health make careful exploration important.

Study each stage's objective before moving quickly. Many obstacles are solved by interacting with the correct environmental targets rather than by defeating every enemy.

Use Bart's x-ray vision when an object or character may be an alien in disguise. Conserve health and lives by learning the layout, watching enemy patterns, and avoiding unnecessary contact.

When a stage contains a timed or target-based task, prioritize the required items first. Exploration is useful, but wandering without tracking the objective can consume limited resources.