Matthew 17:9 - 13

9 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.”

10 And His disciples asked Him, saying, “Why then do the scribes say that Elijah must come first?”

11 Jesus answered and said to them, “Indeed, Elijah is coming first and will restore all things.

12 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.”

13 Then the disciples understood that He spoke to them of John the Baptist.

Jesus' public ministry is coming to an end, He does not want the proof of His divine origin to be publicized before it is the proper time. This event with Him being transfigured and the meeting with Moses and Elijah along with God's statement, proves He is the Son of God, and the Messiah.

The disciples mistake the great prophet to be the one who is to prepare the way for Jesus. They think if they are forbidden to announce Jesus divinity, then why would Elijah whom the scribes are saying is coming first be allowed to announce Jesus divinity.

Jesus is quoting the prophecy of Malachi, (Malachi 4:6) He is to bring a reformation into the lives of the people of Israel. (Luke 1:16 – 17 [And he will turn many of the children of Israel to the Lord their God. 17 He will also go before Him in the spirit and power of Elijah, ‘to turn the hearts of the fathers to the children,’ and the disobedient to the wisdom of the just, to make ready a people prepared for the Lord.” ])

The verse listed in Luke, proves Jesus statement in verse 12, It is John the baptist coming in the spirit and power of Elijah, the leaders of the Jews did not heed his warnings and the was killed by Herod and Jesus says He will follow the same fate as John.

From Jesus explanation in verse 12, the disciples understood He was speaking about John the baptist.