The question was asked, "Why then say the scribes that Elias must first come?" The reason for the question is that Peter, James and John had just seen the Lord coming in his kingdom. They knew from the scribes that Elijah had to come before the Lord returned and that he hadn’t come yet.

The Old Testament prophesies of the messenger that would herald the Lord’s coming are in Mal 3:1 and Is 40:3-4. If you check the context of those references, you see that they deal with the Lord’s Second Coming. They deal with an event that hasn’t taken place yet. The forerunner of that event is Elijah as you see in Mal 4:5, Rev 11 and Matt 17:3.

But Jesus told the disciples that Elias had already come "and they knew him not." The disciples understood that he was speaking of John the Baptist. How did they figure that out?

Matthew said that John the Baptist fulfilled the prophecy of Isaiah 40:3 [see Matt 3:3-4] which is a prophecy about Elijah. Yet Matthew did not quote the whole passage, because only a part of what Jesus came to do was completed at his first coming. The part about straightening out the crooked places, exalting the valleys and bringing the mountains low was not fulfilled — and won’t be until the Lord returns.

In John 1:19-13, John the Baptist was asked if he were Elijah and he flatly denied it. In fact he wasn’t Elijah. However, he did "go before [Jesus] in the spirit and power of Elias … to make ready a people prepared for the Lord," [Lk 1:13-17]. So, his commission was very similar to Elias’.

Why the similarity? God, in his sovereignty, left the opportunity for the Jews to accept Jesus Christ, his Son, as their Messiah and King. In his foreknowledge, he knew they wouldn’t. But in his mercy, he gave them fully the opportunity to repent. Had they done that, then John the Baptist would have fulfilled those things that Elijah will be coming to do during the tribulation.

Look at Matt 11:12-14. Jesus had been preaching about his coming kingdom. The Jews had to accept it in order for his kingdom to come at that time. If they had accepted it, then Jesus said that John the Baptist would have fulfilled the prophecy concerning Elijah.

As it turns out, the Jews rejected Jesus as their King [Jn 19:15]. Thus, the door began to close on the Holy Spirit’s work with Israel and began to open for the Gentiles [Matt 15:24; Acts 28:24-29; Rom 11; Acts 10; Eph 2:12-19; etc].

After the "fullness of the Gentiles be come in," [Rom 11:24-27] God will send Elijah. Following his 42 months of prophesying, Jesus will return and save Israel [Rev 11; Rom 11].