Why did the disciples ask Jesus, “Then why do the scribes say that first Elijah must come” (Matthew 17:9-13; Mark 9:9-13)? What were their beliefs, and why in the end did they accept John the Baptist as Elijah? Plus how are we also in the dark?
WHY WERE THEY SO UNCERTAIN?
From the intertestamental literature, including certain…Qumran writings, and from the NT it is evident that this rich and varied presentation of one who was to…usher in the day of the Lord issued in the notion of different Messiahs. Not before Jesus of Nazareth…did anyone find it possible to harmonize in one person all the messianic hopes. Occasionally in one simple statement our Lord brought two or more themes of OT messianic prophecy together, as, for instance… “For the Son of man came not to be ministered unto, but to minister, and to give his life a ransom for many” (Matthew 20:28; Mark 10:45). Here the Danielic apocalyptic Son of man and the Isaianic prophetic Servant of the Lord…are brought together.
WHAT WERE THEY EXPECTING?
The idea of the Messiah cannot be confined strictly to…the…anointed king. The term Messiah has been descriptive of all…who was to come from God to fulfill the…deliverance and the promises of a new state of divine blessing. The nature of this deliverance…of the state of divine blessing, and…the Messiah vary greatly…. So greatly…that Messiahs of several sorts with a variety of descriptive names were expected…. The term Messiah enveloped other prophetic figures in the OT, such as Moses’ Prophet “like unto me,” Isaiah’s suffering Servant, Jeremiah’s Branch, Daniel’s Son of Man, and other figures, including the coming of the Lord himself as the deliverer of his people.
WHEN DID JESUS CLEAR UP MOST OF THEIR CONFUSION?
In post-resurrection appearances especially, Jesus is said to have taught his disciples how the OT predictions were fulfilled in himself (Luke 24:27, 44-47; Acts 1:3). Many of these prophecies are declared by the NT writers to be fulfilled in Jesus’ first advent. Others are by Jesus himself related to the current period between the two advents or to the time of his return; if not for their initial fulfillment, certainly for their culmination.
In other words, prophecies often reflect the nature of God, who does not live within the time constraints we do. Biblical prophecies often predict things that will happen even centuries apart. But it sounds like it might all happen at once. Only those who have seen parts of these prophecies already fulfilled would know the difference.
WHAT DID THE DISCIPLES BELIEVE ABOUT ELIJAH?
Based on Malachi 4:5-6,
and also on the fact that Elijah did not die but was taken up to heaven directly (2 Kings 2:9-12), Jewish tradition spoke often of the future return of Elijah. As an example, in the Mishnah (Edduyot 8:7), Elijah will come to settle all disputes and reconcile all discrepancies in the holy books. In that passage of the Mishnah, discussion ensues as to what Elijah will accomplish. At the end of the passage, “The Sages say, [Elijah will come]… to make peace in the world, as it is said…” , followed by quoting the Malachi passage.
He is also involved with the resurrection of the dead in the Mishnah, Sotah 9:15: “The resurrection of the dead shall come through Elijah of blessed memory.”  The resurrection was expected to happen at the end of history, so Elijah here is definitely associated with the end of time. And of course at Passover, an entire place setting is put out for Elijah as well as a special cup of wine, and the door is opened for him to enter. For the hope at Passover is that if Elijah comes, the Messiah himself cannot be far behind.
WHY WOULD JOHN THE BAPTIST SEEM LIKE ELIJAH?
The transfiguration introduced the disciples to Elijah and Moses. So the disciples asked Jesus why the scribes say Elijah is supposed to come first (Mark 9:11-13).
Jesus…first…agrees that Elijah… “will” restore all things, future tense. Then he immediately says that Elijah has already come and suffered…even as Jesus himself will suffer. As to the future, it may well be that Elijah will appear before the second coming of Jesus, which will lead to the final restoration of “all things.” But the restoration will soon begin its preliminary stages through the crucifixion and resurrection of Jesus. In that sense, the apparently contradictory ideas of (1) restoring all things and (2) a suffering and dying Messiah, are reconciled. The first stage of restoration happens through the death of the Messiah, and John the Baptist is Elijah come back. In the same sense that the Messiah could be thought of as David resuming his rule — a “greater David” — so John the Baptist was a “greater Elijah.”
ESCHATOLOGY IN THE BIBLE
Do you ever study eschatology? This is one of the most difficult subjects to discern correctly. It’s not that obvious whether we should be pre- or post-trib, pre- or post-millennial. We need to study and discuss it, but not assume we have all the answers.