We generally write "What does she have for breakfast?" so my question is why can't we write What does she has for breakfast?
See this answer . g. g.
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See this answer.
Edit: To add to the above, when you have two verbs together in a sentence, the second will always be the bare infinitive (e.g. "have"), the to-infinitive (e.g. "to have"), or the present participle (e.g. "having").