You are going to prepare tax returns for both Massachusetts and Illinois. You will pay taxes in Massachusetts for all of the income you earned in Massachusetts, regardless if it was the 1099-NEC or W-2, and regardless of where you lived.
All of the income you earned in MA while living in IL will be included on the IL tax return (this sounds like the 1099-NEC that you got); however, you will get credit for the tax paid to MA on the IL tax return.
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