Reaction of the Disciples to the Transfiguration – by Dr. Thomas O. Figart – 
Matthew 17:6-8
17:6-8 “And when the disciples heard it, they fell on their face, and were very much afraid, And Jesus came and touched them, and said, Arise, and be not afraid. And when they had lifted up their eyes, they saw no man, except Jesus only.”
Fear resulted primarily as a result of the manifestation of the glory of the Lord in the cloud, and secondarily, in the response of God to Peter’s suggestion. The glory of God in itself is awesome enough, as Isaiah found it to be in Isaiah 6:3-5, or Ezekiel in Ezekiel 1:28. But the disciples also reacted to the rebuke by God that this One, His beloved Son is preeminent! Moses had glory, but Christ is worthy of greater glory; Moses was faithful as a servant in his house, but Christ as Son over His house (cf. Hebrews 3:1-6). As for Elijah, Hebrews 1:1-2 reminds us that God spoke in time past in the sphere of the prophets, a servant-revelation, but He has spoken in these last days in a Son-revelation! It is no wonder then, that God wanted Christ to be preeminent in the Translation.
Our Lord graciously calmed their fears with His touch and His gentle words. Yet, even as they lifted up their eyes, Moses and Elijah were gone, and they saw Jesus only!
Exhortation to tell no man. Matthew 17:9
17:9 “And as they came down from the mountain, Jesus charged them, saying, Tell the vision to no man, until the Son of man be raised again from the dead.”
Five times in Matthew Jesus prohibited the telling of His experiences or exploits, each with a distinct emphasis. In 8:4 the cleansed leper was told to tell no man, but to go directly to the priests and offer the prescribed gift, so the priests would know that the man was actually healed of leprosy, and thus that Jesus Who healed him was God! Then the man was apparently free to tell everyone. In 9:30 it had to do with the healing of two blind men. There, His reluctance at making their healing known had to do with the possibility that the crowd would take Him by force and make Him king, similarly to John 6:15. In Matthew 12:16 after the healing of the multitudes, Jesus withdrew Himself and charged them that they should not make Him known. In this case it was because the Jews wanted to destroy Him, as 12:14 indicates. The fourth occasion is in 16:20, and by this time the longsuffering of Jesus had come to and end with official Israel and He had already rejected them (cf. 11:20-24), refusing to give any further signs than that of the prophet Jonah (12:38-45; 16 ;1-5). Thus, in 16:20 Jesus was about to give the prophecy of His own future suffering as the Savior, not as the ruling Sovereign. The account in Luke 9:21-22 makes this connection clear as the reason for the command to tell no one.
It is not strange, therefore, that at His Transfiguration He commanded them for the last time to tell no man until after His resurrection. Who among His disciples would believe such a vision after His prediction of His death in 16:21-23? Even if they did, any hope of His becoming a glorified Messiah would be dashed to pieces by His death. But after the resurrection the hope of His glorious return would elate and encourage all who knew of the Old Testament promises of His coming back to earth to establish His Kingdom of glory!
The Explanation Concerning Elijah. Matthew 17:10-13
17:10-13 “And his disciples asked him saying, Why then say the scribes that Elijah must first come? And Jesus answered and said unto them, Elijah truly shall first come and restore all things. But I say unto you, that Elijah is come already, and they knew him not, but have done unto him whatsoever they desired. Likewise shall also the Son of man suffer of them. Then the disciples understood that he spoke unto them of John the Baptist.”
Having noted all these things, it does at first seem strange that Jesus should affirm in no uncertain terms the future fulfillment of Malachi 4:5-6 by the historical Elijah who will return before the Messiah and “restore all things.” The answer lies in the previous statements of Christ. The “if” clause in 11:14 is a first class conditional clause denoting assumed reality. If they had willed to receive John as Elijah, he would have been, and presumably they would also have received Christ as their Messiah/King. But in that same paragraph (11:15-19) the truth was that the Jews rejected the forerunner of the Messiah. So then, here in Matthew 17:10-13 Jesus gives the result; the Jews did to John whatever they wanted (which was to behead John) and the Son of man will likewise suffer of the Jews (by crucifixion). Having rejected the Person of the King, they automatically refused His rulership over them.
Some commentators question how much John the Baptist knew, since he denied that he was Elijah in John 1:21, yet he affirmed that he was fulfilling Isaiah 40:3 as the forerunner of Christ. It is sufficient to say that there were some things John the Baptist did not comprehend. The beginning verses of Matthew 11 state directly that John was unsure of Christ’s messiahship, since hem the forerunner of Messiah was in prison. He even went so far as to ask: “Do we look for another?” Just how much his messengers were able to comfort him is unknown. Nevertheless, all the statements about John the Baptist actually being Elijah were hypothetical, being contingent upon the nation of Israel’s reception of Jesus as their Messiah.
This takes us back to the old question: “Could Christ give a legitimate offer of the Kingdom, knowing that the Jews would reject it?” The answer is yes, just as Jehovah made a genuine offer to Adam and Eve of eternal bliss in Eden, contingent on their obedience. Did God know they would sin? Of Course God knew, but this did not make the offer insincere, nor did it mean that God’s “Plan A” failed and that He had to go with “Plan B.” The rejection of the Kingdom was simply the means for carrying out the original plan of redemption through the crucifixion of the Lamb of God, just as really as the allowing of the sin of Adam and Eve was part of that plan. We must realize that, “In the fulness of time,” when we get to heaven, all the unknown details of God’s eternal purpose will be made known to us!