See also Mark 9:11-13.
Why then say the scribes ... - The disciples appear to have been satisfied now that he was the Messiah. The transfiguration had taken away all their doubts, but they recollected that it was a common doctrine among the Jews that Elijah would appear before the Messiah came, and they did not then recollect that he had appeared. To this difficulty the word then refers. “We are satisfied that thou art the Christ, but Elijah has not yet come, as was expected; what, then, is the meaning of the common opinions of our learned men, the scribes? Were they right or wrong in their expectation of Elijah?” See the notes at Matthew 11:14.
Elias truly shall first come, and restore all things - He did not mean by this that Elijah was yet to come, for he tells them immediately Matthew 17:12 that he had come; but he meant to affirm that it was a true doctrine which the scribes taught, that Elijah would appear before the coming of the Messiah. To “restore” means to put into the former situation. See Matthew 12:13. Hence, it means to heal, to correct, to put in proper order. Here it means that Elijah would put things in a proper state; he would be the instrument of reforming the people, or of restoring them, in some measure, to proper notions about the Messiah and preparing them for his coming. Before the coming of John their views were erroneous, their expectations were worldly, and their conduct were exceedingly depraved. He corrected many of their notions about the Messiah (see Matthew 3), and he was the instrument of an extensive reformation, and thus restored them, in some degree, to correct views of their own system and of the Messiah, and to a preparation for his advent.
Elias is come already - That is, John the Baptist has come, in the spirit and power of Elias. See Luke 1:17.
They have done unto him whatsoever they listed - The word “list” is an old English word, signifying to choose, to desire, to be inclined. See Judges 3:8. It means, here, that they had done to John as they pleased; that is, they had put him to death, Matthew 14:10.
Mark adds Mark 9:12 that Jesus told them that it was “written of the Son of man that he must suffer many things, and be set at naught.” This was written of him particularly in Isaiah 53:1-12. To be set at naught is to be esteemed as worthless or as nothing; to be cast out and despised. No prophecy was ever more strikingly fulfilled. See Luke 23:11, Luke 23:14-21. This narrative, with some additions, is found in Mark 9:14-29, and Luke 9:37-43.