The color of fuel indicates the fuels age. The dark color is coming from Asphaltenes…this takes years to develop.
To fix it remove the water first. Once the water is gone he can then filter out the solids. BUT filtering may take LOTS of filters so we are back to how many gallons do we have?
If you have an older engine with mechanical injection as long as the big solids are removed the engine will be fine…but get the water out…no engines like water.
If you have hundreds of gallons you need to use an additive to speed up the cleaning. http://dieselcraft.com/fuel-tank-cleaning-chemicals/