'Thoughts' in the Bible

They show that the essential requirements of the Law are written in their hearts; and their conscience [their sense of right and wrong, their moral choices] bearing witness and their thoughts alternately accusing or perhaps defending them

on that day when, as my gospel proclaims, God will judge the secrets [all the hidden thoughts and concealed sins] of men through Christ Jesus.

the mind of the flesh [with its sinful pursuits] is actively hostile to God. It does not submit itself to God’s law, since it cannot,

For who has known the mind of the Lord, or who has been His counselor?