The lysosome functions in a cell like the does in our bodies.

Lysosomes remove waste at a cellular level.
They contain digestive enzymes, so they're like the digestive system.
The stomach digests food, so lysosomes could be considered like the stomach.
But then again, so do the intestines, small and large.
Since the stomach doesn't also work to remove waste though, I'd say the answer is probably large intestine, which finishes the digestive process and removes waste material.

Are their choices to the question?