What does Matthew 17:12 mean?

The disciples are asking Jesus about the return of Elijah the prophet. The scribes teach from Malachi 4:5–6 that Elijah must return before the Messiah can come. Now, they know Jesus is the Messiah who has come to earth (Matthew 17:1–11). So, what about Elijah? They had just seen Elijah talking with Jesus during the transfiguration, but was that his "return"?

Jesus has confirmed that the prophecy is true and adds now that it has already taken place. Elijah has already come, in the prophetic sense which was predicted. Jesus says the reason the scribes are still insisting that Elijah is yet to come—meaning that Jesus must not be the Messiah—is that they did not recognize that John the Baptist was "the Elijah who was to come" (Matthew 11:14). The people are treating the prophecy as a superstition—that Elijah will be raised from the dead. This is why John the Baptist denied being Elijah when questioned by the Pharisees (John 1:20–21).

Although John's ministry was successful in leading many in Israel to repentance (Luke 1:17), he was ultimately rejected by most of Israel's religious leaders. Israel's political leaders, in the form of Herod Antipas, did to John whatever they pleased as the political leaders of old had done to the prophets of old. Herod had John arrested and eventually executed (Matthew 14:1–12).

Jesus concludes by saying the same—rejection followed by execution—will happen to Him. He will go unrecognized for who He truly is. He will be rejected, and He will suffer at the hands of the religious and political leaders of Israel (Isaiah 53:3–6). Jesus is not disguising His words to the disciples about His approaching suffering, death, and resurrection. They are still struggling to understand what this means and how the Messiah could possibly die in such a way.