The Brookhaven Experiment: Mobile is a more streamlined, arcade-style experience. The game features five maps, each of which has an end boss that can be defeated to unlock the next map. Maps can also be played after the end boss has been defeated for high score, with each wave escalating in difficulty, similar to the survival mode of Brookhaven PC.

Instead of an inventory, upgrades are acquired in each map as the player defeats waves, with better scores leading to better and better upgrades. Good scores also allow the player to acquire high-powered temporary weapons, which are discarded when they run out of ammo, and throwable grenades.