I'm not sure where you came up with this rule about the verb not taking the s, but the verb will agree with the subject (What is he doing here?) or take the third-person singular, as in "What happens next?"
Perhaps you are thinking about situation in which you have the verb "to do" in the question: What did he do? What did happen after that?
When you have a form of the verb "to do," it will be conjugated, but the other verb will remain in the bare infinitive form - do/happen/etc. That applies to normal declarative as well: It did happen that way! He did not do that.