What happens to bacteria after it is flushed down the toilet?

Fecal matter/rotten meat doesn't turn into maggots. Flies and bacteria are separate life forms. The biogenesis theory of decomposition is pretty much ancient now.

Rotten meat decomposes in the presence of oxygen (most of the time) because of the bacteria that pervades the air (and most other places.) Maggots appear on rotting matter because living flies are attracted to the rotting substance. They eat some of it and lay eggs, which hatch and grow into maggots.

I'm afraid that your final question is moot as none of the things you've mentioned are 'mutant forms' of bacteria.

As for the title question. It goes down the toilet. There's little else. Some of it could die due to being broken apart/deprived of oxygen/food. Some of it could continue living and growing wherever it ends up. There's no simple answer.

Sewage is treated at a sewage treatment plant. Google it sometime. Feces and spoiled meat do not turn into maggots. Flies lay their eggs in feces and spoiled meat and maggots are fly larvae so in time, the adult flies emerge from the larvae and fly off.

What do you mean "what OTHER mutant form..". You haven't named a mutant form of any thing to begin with.

Things don't just "turn" into maggots; maggots are insects that are born from insect parents. Feces or rotten meat would attract insects, and could grow eukaryotes like mold or fungus.

It is sent to a sewer pond where it is treated.