9a And as they were coming down the mountain 10 the disciples asked him, "Then why do the scribes say that first Elijah must come?" 11 He replied, "Elijah does come, and he is to restore all things; 12 but I tell you that Elijah has already come, and they did not know him, but did to him whatever they pleased. So also the Son of man will suffer at their hands." 13 Then the disciples understood that he was speaking to them of John the Baptist.
Daily Quote from the early church fathers:
John fulfills Elijah's prophetic ministry, by John Chrysostom, 547-407 A.D.
"They did not know this from the Scriptures, but the scribes used to tell them, and this saying was reported among the ignorant crowd, as also about Christ. Therefore the Samaritan woman also said, 'The Messiah is coming; when he comes, he will show us all things' (John 4:25). And they themselves asked John, 'Are you Elijah or the prophet?' (John 1:21). For this opinion was strong, as I said, both the one about Christ and the one about Elijah, but they did not interpret it as it should have been. For the Scriptures speak of two comings of Christ, both this one that has taken place and the future one. Paul spoke of these when he said, 'For the grace of God has appeared for the salvation of men, training us to renounce irreligion and worldly passions, and to live sober, upright and godly lives in this world' (Titus 2:11-12).
"Behold the first advent, and listen to how he declares the coming advent: 'Awaiting our blessed hope, the appearing of the glory of our great God and Savior Jesus Christ' (Titus 2:13). The prophets also mention both advents; of the one that is second they say that Elijah will be the forerunner; John was forerunner of the first, John whom Christ also called by the name Elijah, not because he was Elijah but because he was fulfilling Elijah's ministry. For just as Elijah will be the forerunner of the second advent, so John was of the first. But the scribes, confusing these things and perverting the people, mentioned that coming alone, the second one, to the people, and said, 'If this is the Christ, Elijah ought to have come first.' That is why the disciples also say, 'Then why do the scribes say that first Elijah must come?'"
(excerpt from THE GOSPEL OF MATTHEW, HOMILY 57.1)