How does a carbon atom get from the atmosphere to a fossil fuel?

Fossil fuels were at one time living organisms (usually plants). The plants took in carbon dioxide from the air and then release oxygen. The carbon is stored in the plant. When the plant dies, the carbon stays in it, throughout the transformations it goes through to become a fossil fuel.

When the fuel is burned, the carbon is release in the burning process, usually in the form of carbon dioxide.