Had better is an idiomatic verb phrase meaning ought to, must. It resembles an auxiliary verb in that its form never changes to show person or tense and that it cant follow another verb in a phrase (that is, you cant say He will had better leave, for example).
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When speaking, people have a tendency to leave out had: You better clean up your room! But in writing, you had better keep had, either in full or as a contraction: You had better not do that or Youd better not do that.