Current theory on fatty liver disease:

Caused by these three, either alone or in combination:

Choline-deficient diet
High sugar diet
High amounts of alcohol

As high amounts of sugar enter the body, the pancreas and the liver's job is to prevent blood sugar levels from getting too high, or the body would be damaged, or could even die. The pancreas creates insulin, which extracts sugar from blood, into the tissues, protecting the body from sugar damage. The liver tries to prevent too much sugar from reaching the blood in the first place by converting it to fat via lipogenesis. If the sugar is small enough, this isn't a problem. If the sugar is too high, it's more difficult for the liver to remove this fat.

Choline is necessary for the packaging and export of fats from the liver to the tissues, this is what LDL is: a lipoprotein sphere designed to transport triglycerides. HDL is transport of fat from tissues to the liver, LDL is transport of fat from liver to tissues. Liver cell death has been shown to occur with the absence of choline, making the liver's job harder.[1]

YET, a problem arises when TMAO comes into play. TMAO (trimethylamine nitric oxide) is a chemical created by bacteria, which has the effect of reducing bile created by the liver. Why? Because these bacteria consume choline, and choline is necessary to create bile, so the bacteria have evolved to create a substance that reduces the creation of bile, which is toxic to most bacteria and increases the difficulty of survival.

Studies have shown that eating choline-filled foods often increases TMAO levels, probably because it feeds these bacteria. But, if choline is necessary to create bile, to prevent and reverse fatty liver, should choline be eaten or not?

It's been shown that after a kidney transplant, TMAO levels lower back to normal levels.[2] Why? It seems as though people with fatty liver may also have weaker kidneys. Is it possible that because the liver has weakened, higher amounts of sugar have escaped into the blood, and damaged the kidneys? It has indeed been shown that high sugar in the blood damages kidney nephrons. [3]

My theory:

Consume CDP-Choline, a form of choline harder for bacteria to digest
Exercise. It's healthy for both the liver and the kidneys and has been shown to improve microbiome regardless of diet
Eat eggs and/or liver. High in b12, folate, and choline
Eat fish or take an Omega3 supplement, minimum of 400mg Omega3 Fatty acids. Resolves inflammation and protects kidneys

[1] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3601486/

[2] https://pubmed.ncbi.nlm.nih.gov/26751065/

[3] https://www.cdc.gov/diabetes/managing/diabetes-kidney-disease.html

[4] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5339475/