Puzzles are the foundation of Cell Machine. Puzzles have placeable and unplaceable areas. Within the placeable area, there will be cells that the player can move around. Within the unplaceable area, there will usually be some form of obstacle(s), and there will always be one or more enemy cells. The goal of the player is to find the arrangement of the cells within the placeable area that defeats the enemy cell. The player does all of this while the simulation is not running, and then turns on the simulation. If during the simulation, the enemy cell is destroyed, the player wins! Otherwise, the player will reset the grid and try something else. Note that in this sense the word "player" means the actual person behind the screen, not the player cell present in some remakes.