In Rescue: The Beagles the player controls animal activist Edwin or Nicole to rescue beagles who were part of a cargo inside an airplane, heading to the CutLab testing facility. The plane crashed and the contents have been scattered above the areas of the Amita range. The activists are not alone - the lab sends out a team as well to retrieve its testing material and kill the rest.

Players control one of the two activists in different levels that scroll to the right at a fixed pace. The environment is made up of different background layers that move at different speeds. Edwin or Nicole can climb or descend to any layer when it is within reach, or use a rope to climb to high areas or a parachute to float down. Both are not standard equipment and need to be picked up first before they can be used. The gameplay is very fast as no beagles are allowed to reach the left side of the screen. Meanwhile, players take out doctors and biohazard researchers by collecting owls as ammunition. There are also medkits that restore the health of hurt puppies and provide additional points.

Each level has an increased amount of beagles needed to be rescued, with different types of enemies. A large part of the gameplay is also based around timing and watching the different background layers' speed to decide when to climb or when to descend. The maps are procedurally generated based on the Markov chain.

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