The question begins with "then," tying it to what the disciples had just seen and heard. Gill says, "The disciples having just now seen Elias, are put in mind of this tenet of the Scribes." Barnes puts their thought this way: "We are satisfied that thou art the Christ. But Elijah is not yet come, as was expected." Gill adds that the scribes used this teaching against Jesus, arguing "if he was the Messiah, Elias would be come." The disciples wanted to know how the scribes' teaching fit with what they now believed about Jesus.

Jesus answered directly. First He affirmed the teaching: "Elias truly shall first come, and restore all things" (Matthew 17:11). Then He said, "Elias is come already, and they knew him not, but have done unto him whatsoever they listed," and added, "Likewise shall also the Son of man suffer of them" (Matthew 17:12). "Then the disciples understood that he spake unto them of John the Baptist" (Matthew 17:13). Mark adds that it happened "as it is written of him" (Mark 9:13).

The scribes, experts who taught the law of Moses, based their teaching on Malachi 4:5: "Behold, I will send you Elijah the prophet before the coming of the great and dreadful day of the LORD." Barnes says "it was a common doctrine among the Jews that Elijah should appear before the Messiah came," and on Matthew 17:11 he calls it "a true doctrine which the scribes taught." Gill says the Jewish expectation of Elias coming with the Messiah "is founded upon a mistaken sense of Mal 4:5," because, as he explains on Matthew 17:11, the prophecy is "not of Elias the Tishbite, in person, but of one that was to come in his power and spirit." "Elias" is the Greek form of Elijah.

Before John was born, the angel said he would go "in the spirit and power of Elias" (Luke 1:17). Jesus had already told the crowds about John, "this is Elias, which was for to come" (Matthew 11:14).

Jesus does not brush aside the Scripture behind the scribes' teaching. He affirms Malachi's promise and shows that God kept it in John the Baptist, though people "knew him not" (Matthew 17:12). God keeps His word, but not always in the form people expect.

Then Jesus ties John's suffering to His own: "Likewise shall also the Son of man suffer of them" (Matthew 17:12). The glory the disciples saw on the mountain did not cancel the cross. It came right alongside His command to tell no one "until the Son of man be risen again from the dead" (Matthew 17:9).