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This will eliminate the rust, and it works no matter whether you have a few spots or the entire skillet has gotten rusty. Get a big pot large enough to hold the skillet. Fill it with a solution of half white vinegar, half water. Place the skillet in the pot and make sure it's completely submerged. Soak it for at least 3 hours so the vinegar has time to dissolve the rust.  When you remove the skillet, check for rust. If you still see rust spots, use a scrub brush to scrub them away. Don't soak the skillet for more than 4 hours, or the iron will start to degrade. You just want to soak it long enough to take off the rust. Rinse off all of the vinegar, then use a dish towel to completely dry the skillet. Just like you would for a brand new skillet, use a paper towel to rub lard, olive oil or vegetable oil all over the skillet. This will become the skillet's new seasoning. Put it in an oven preheated to 350 °F (177 °C). After 2 hours, remove the skillet and let it cool completely. Coat it in another layer of oil, bake for 2 hours, and allow it to cool again. The once-rusty skillet should now have a protective layer of seasoning.

Summary:
Soak the skillet in a vinegar solution. Rinse and dry the skillet. Coat it with fat. Bake the skillet for 2 hours. Repeat the process.