Waking Mars is an adventure game in which you control a jetpack-equipped protagonist through a cave system located on Mars. In 2097, life was discovered inside a cave system known as Lethe; thus a mission was sent to research the new discovery. As he learns the first secrets of this martian underground ecosystem, Liang — one of the researchers — becomes trapped inside the Lethe caves. In order to make his way to safety, the protagonist is forced to go deeper and deeper into the caves, which gives him the opportunity to make numerous scientific discoveries.
Learning the way the ecosystem functions is the key mechanic of this game. Understanding the behaviours and interactions between the various Martian lifeforms is the only way the player character can advance from one location to the other. Using his understanding, Liang can influence, even control, the ecosystem. While the initial areas are simple to complete, as the game goes on, more and more creatures are introduced which complicate matters for the protagonist. Some of the choices can even irrevocably alter the game world, as progress is saved continuously.