There is the hard way and the easy way. Or maybe the easy way will turn out to be a hard way, too.
Theoretical easy way: disconnect the hot or cold plumbing and pour two pints of drugstore peroxide into the heater. Don’t bother trying to drain it. The peroxide will take care of any cooties growing in the heater.
The harder way: Use the Water Heater Basics link on the left side of the Tank index, and when you get there, click on Know-How, and following the instructions, replace the drain valve with a brass ball-valve drain assembly, and then try flushing again.