Old English hu, from West Germanic *hwo- (cf. Old Saxon hwo, Old Frisian, Middle Dutch hu. Dutch hoe, German wie, Gothic hvaiwa "how"), from common PIE interrogative pronomial stem *kwo- (see who). How come? for "why?" is recorded from 1848. And how! emphatic, first recorded 1865. The formulation was common in book and article titles by then, e.g. The National Debt, and How to Pay It), but Pennsylvania writer Bayard Taylor, in whom it is first recorded, seems to regard it as a German or German-American expression.
Native American greeting, Siouxan (cf. Dakota hao, Omaha hau); first recorded 1817 in English, but noted early 17c. by French missionary Jean de Brebeuf among Hurons as an expression of approval (1636).
What is that? what is the reason?: ''Change of plans. We move today'' ''How come?'' (1848+)