There are billions of bacteria living in your mouth all the time. They're all constantly reproducing, peeing, and pooping. That waste smells bad.

During the day you are generating spit and swallowing, which helps to keep the bacteria populations down, and continually washes the waste away as it's produced, or at least before it can build up too much.

At night, you stop generating as much spit and you don't swallow. So all the bacteria can multiply and their pee and poop can also accumulate. That's what morning breath is. Bacteria colonies and their waste.