17:9 This is the last of five times Matthew recorded Jesus telling His disciples to keep silent (cf. 8:4; 9:30; 12:16; 16:20). This time He told them that they could tell others after His resurrection since this is the first time He told them to keep quiet after He had revealed that He would rise again. The proclamation of the King and the kingdom would begin again after the Resurrection. Temporary silence was important because of popular political views of Messiah and because the signal proof of Jesus' messiahship would be His resurrection, the sign of Jonah.
17:10 The disciples in view seem to be Peter, James, and John (cf. v. 14). It seems unlikely that the disciples viewed Elijah's appearance in the Transfiguration as the fulfillment of Malachi 4:5-6. If they did, their question would have been, why did Messiah appear before Elijah when the scribes taught the reverse order of appearings? Moreover Elijah's appearance in the Transfiguration did not turn the hearts of the people back to God.
Peter, James, and John's question evidently arose over an apparent inconsistency involving Jesus' announcement of His death. Elijah's appearance on the mountain probably triggered it. Elijah was to come and turn the hearts of the people back to God before Messiah appeared (Mal. 4:5-6). If that restoration happened, how could Jesus die at the hands of Israel's leaders (16:21)? The disciples were struggling to understand how Messiah's death could fit into what they believed about the forerunner's ministry.
Notice that from the Transfiguration on these disciples had no further doubts about Jesus' messiahship.
17:11-12 Jesus confirmed the scribes' teaching about Elijah coming, but He said another factor needed consideration. John the Baptist's ministry had been a success as far as it had gone (cf. 3:5-6; 14:5), but he had "restored all things"to only a limited degree. The scribes perceived the ministry of Messiah's forerunner correctly, but they did not realize that John the Baptist had been that forerunner (11:10). Elijah had already come in John the Baptist. However, Israel's leaders had rejected him, and he had died without accomplishing the complete restoration of Israel. John had not fulfilled his mission but died doing so. Likewise Jesus would die at His enemies' hands without fulfilling His mission of establishing the kingdom. John had restored all things as much as he could and yet died. Jesus, too, would fulfill His mission as much as He could and yet die. This was the answer to the disciples' question.
"A suffering Forerunner is to be followed by a suffering Messiah."676
"In other words, just as the messianic forerunner's coming had two phases: John the Baptizer (one to suffer and die), and Elijah the Prophet (one of restoration and glory), so also would the Messiah's coming. The response to the forerunner foreshadowed the response to the Messiah and necessitated the postponement of the fulfillment specifically promised to national Israel."677
God predicted through Malachi that a Jewish revival would precede Messiah's kingdom, and the revival did not come. Consequently that revival and the kingdom must still be future.
17:13 The disciples now understood that John the Baptist fulfilled the prophecy about Elijah returning. However, their continuing problems with Jesus' death seem to indicate that they did not really understand that He had to die. This incident reveals another step of understanding that the disciples took, but it was only a small step.