MA taxes income earned from a MA source or a MA job. Since you worked for a MA organization, you have MA income and must pay MA tax. You need to fill out the MA non-resident form first to create the tax liability. THEN prepare your resident state return and it will generate a credit for your income already being taxed. The credit will be the lower of the state tax liabilities on the same income. You may owe your resident state.
It sounds like your income was all MA based. Unless you travelled to other states to perform work, which you don't mention.
Please see Form 1-NR/PY Instructions See page 3, number 2 as it describes what I believe are your circumstances.
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