Steps of the digestion system Lets say you just ate a taco and it is now passing through your digestive system. First the taco goes into your mouth, then it goes through your throat and ends up in you stomach. After its broken down in the stomach it goes through your small intestine to be broken down even more. Then finally after your small intestine it goes to your large intestine which takes the water out of the food. After that it goes to your anus then your rectum and the stuff that is not needed comes out as poop.