"While he [i.e., Peter] was still speaking, behold, a bright cloud overshadowed them, and suddenly a voice came out of the cloud, saying, 'This is My beloved Son, in whom I am well pleased, Hear Him!' And when the disciples heard it, they fell on their faces and were greatly afraid. But Jesus came and touched them and said, 'Arise, and do not be afraid.' When they had lifted up their eyes, they saw no one but Jesus only. Now as they came down from the mountain, Jesus commanded them, saying, 'Tell the vision to no one until the Son of Man is risen from the dead.' And His disciples asked Him, saying, 'Why then do the scribes say that Elijah must come first?' Jesus answered and said to them, 'Indeed, Elijah is coming first and will restore all things. 'But I say to you that Elijah has come already, and they did not know him but did to him whatever they wished. Likewise the Son of Man is also about to suffer at their hands.' Then the disciples understood that He spoke to them of John the baptizer."
Matthew indicates that God interrupted Peter before he was finished speaking. "A bright cloud overshadowed them; and suddenly a voice came out of the cloud, saying, 'This is My beloved Son, in whom I am well pleased'" (Matt. 17:5). It is probable that this cloud was similar to the one that guided the Israelites during their years of wandering in the wilderness (cf. Num. 9:15ff). On this occasion, God the Father once again stated His pleasure in Jesus as He declared His Son's divinity (cf. Matt. 3:17).
The command from the Father to "Hear Him [i.e., Jesus]" seems to offer some insight as to why Moses and Elijah were the ones who appeared with Jesus on this mountain. Moses was the greatest human representative of the law and Elijah was the greatest human representative of the prophets, yet they were both inferior to Christ! In spite of their greatness, they yielded their positions to Christ. He is the greatest lawgiver and prophet of all time! People should listen to and obey Jesus and refrain from going back to Moses and Elijah as if they were equal to or superior to Christ. Jesus' words are to have preeminence over the words of the great lawgiver and prophet of old. The old law would soon be nailed to the cross (cf. Col. 2:14); it would be removed and the new law would be established (cf. Heb. 8:13; 10:9,10). Those who are wise will hear and heed the Christ!
The apostles' response to the voice of the Father is extreme fear. They appropriately fell on their faces. However, the tender touch of Jesus and His words of comfort calmed their fears. As they looked up, they observed that only Jesus remained.
Jesus then commanded them in Matthew 17:9 - "Tell the vision to no one until the Son of Man is risen from the dead" (cf. II Pet. 1:16-18). If they had attempted to tell it at this time, problems would have resulted. Envy would have been created among the apostles, and the common people would have largely rejected such a story as outrageous.
These three apostles obey Jesus' command but ponder amongst themselves as to what exactly Jesus meant by His reference to His resurrection from the dead (cf. Mark 9:10). Since Jesus spoke in parables and used metaphors frequently, they evidently believed His words on this subject to be figurative.
As they came down from the mountain, the apostles asked - "Why then do the scribes say that Elijah must come first?" (Matt. 17:10). Peter, James, and John had just seen Elijah on the mountain, but if Jesus was the Messiah, then they couldn't figure out why He had preceded Elijah's appearance.
The meaning of Matthew 17:11 is not that Elijah was yet to come (cf. 17:12) but that the doctrine which the scribes taught was in fact true (cf. Mal. 4:5,6). "Elijah" would restore all things in that he would prepare the way for the Messiah; he would try to reform the people and get things in order (cf. Mal. 3:1; Matt. 3:1ff).
"But I say to you that Elijah has come already, and they did not know him but did to him whatever they wished" (Matt. 17:12). The prophesied "Elijah" had already come, yet he was unrecognized and treated shamefully. "Likewise the Son of Man is also about to suffer at their hands" - The religious leaders would have Jesus crucified in less than a year.
The apostles then understand that the prophesied "Elijah" was none other than John the baptizer.