Some of the greatest adventures that kids have growing up occur in their imaginations as they play with their toys. Toy Commander is a game that attempts to capture these adventures in an interactive, three dimensional world. The player's perspective is that of the toy vehicles that inhabit a house. The various gameplay areas are all based on rooms in this giant house.

Gameplay in Toy Commander is mission based. In each mission, the player controls one or more toy vehicles to accomplish certain objectives. The objectives in each mission vary widely. In some missions, the player must drive an army truck and shoot things, in some it is necessary to fly helicopters to pick up and drop off objects, and in some the player races against computer-controlled vehicles.

There is a storyline that ties together the missions in the single player mode. A coalition of old toys has started a rebellion against the new toys in the house. An evil Teddy Bear, the Toy Commander, is leading this rebellion. It's the player's job to stop him. In each mission, the basic goal is to complete the task in as short a time as possible. If the player meets a certain time goal, the mission is completed. By completing four missions, the player gets to challenge the boss character in the room. If the boss is successfully destroyed, he will assist the player character in the final fight against the Toy Commander.

In addition to the single player mode, there is a 4-player simultaneous deathmatch mode.