Why then ( οὖν) say the scribes that Elias must first come? The illative particle "then" shows that the apostles' question arose from something immediately preceding. The connection seems to be this: Elias had just appeared and then had vanished again; how could this visitation be reconciled with the scribes' interpretation of Malachi's prophecy?
If Elias was to come before the advent of Messiah, and Jesus is the Messiah, how is it that he has only now shown himself? If he has a work to do on earth, how could he do that when his sojourn was limited to a few minutes' duration, and to the view of so few witnesses?
Malachi had spoken of the Messenger who was to precede and prepare the way for Messiah; he had said, "Before the great day of the Lord, I will send you Elijah the prophet" (Malachi 3:1; Malachi 4:5); and the learned among the Jews interpreted these two passages of his appearance in person to herald the approach of Messiah.
Hence the perplexity of the apostles, they, like the scribes, not distinguishing the two advents of Christ, and the double allusion in the prophet's announcement—the "Messenger" in Matthew 3:1 being a different personage from "Elias" in Matthew 4:5, though of the same power and spirit.
Christ explains the difficulty in the two next verses.