The confusion takes place when John the Baptizer is believed to be Elijah. Elijah was never promised before the First Coming of the Christ, but before the Second Coming, which takes place either right before or in the Tribulation. In the same way Jesus did not set up his kingdom in his first coming, but came to be a sacrificial lamb.

A forerunner was predicted before the First Coming of the Messiah in Malachi 3:1 and Isaiah 40:3-5. This is what was fulfilled by John the Baptist in Matthew 3:1-6; 11:7- 10; and John 1:23. John the Baptizer fulfilled those prophecies before the First Coming but he was NOT Elijah.

In typology John came "in the spirit and power" of Elijah who has come and is yet to come.

Malachi wrote of both messengers, one for the first coming and another the second. Each would have similarities.

Mark 1:2-4 As it is written in the Prophets: "Behold, I send My messenger before Your face, who will prepare Your way before You." "The voice of one crying in the wilderness: 'Prepare the way of the Lord; make His paths straight.” John came baptizing in the wilderness and preaching a baptism of repentance for the remission of sins.

John wore a garment of camel's hair and a leather belt the same attire that Elijah wore (2 Kings 1:8), emphasizing the similarity of his mission to that of Elijah's. John’s message is to prepare, get right, repent.

His ministry is one of reconciliation: Luke 1:17: "He will 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," in fulfillment of Malachi 4:6, to avert the judgment of the earth Malachi warned of. But He would not literally be Elijah.

As John the Baptist was the forerunner of the Messiah's First Coming. Elijah the Prophet will return to do his work of restoration and be the forerunner of the Messiah's Second Coming.

John the Baptist was Elijah in a certain sense according to Jesus:

Matt 11:7-15 "What did you go out into the wilderness to see? A reed shaken by the wind? "But what did you go out to see? A man clothed in soft garments? Indeed, those who wear soft clothing are in kings' houses. "But what did you go out to see? A prophet? Yes, I say to you, and more than a prophet. "For this is he of whom it is written: 'Behold, I send My messenger before Your face, who will prepare Your way before You.' (quoting Mal.3:1-3) "Assuredly, I say to you, among those born of women there has not risen one greater than John the Baptist; but he who is least in the kingdom of heaven is greater than he. "And from the days of John the Baptist until now the kingdom of heaven suffers violence, and the violent take it by force. "For all the prophets and the law prophesied until John. "And if you are willing to receive it, he is Elijah who is to come. "He who has ears to hear, let him hear!

Jesus calls him "John," never "Elijah, when he is referring to him directly. Elijah is included with 'all the prophets' who came before John, but John who baptizes is separate. John had the Holy Spirit with him from the womb separating him from the prophets of the Old Testament.

Since Israel rejected the Kingdom - Elijah is yet to come to accomplish the final work of restoration; just as it is written.

Matthew 17:9-13: And as they were coming down from the mountain, Jesus commanded them, saying, Tell the vision to no man, until the Son of man be risen from the dead. And his disciples asked him, saying, Why then say the scribes that Elijah must first come? And he answered and said, Elijah indeed comes, and shall restore all things: but I say unto you, that Elijah is come already, and they knew him not, but did unto him whatsoever they would. Even so shall the Son of man also suffer of them. Then understood the disciples that he spoke unto them of John the Baptist.”

His ministry will be restoration for Jewish family reunion. Jesus said "Do you suppose that I came to give peace on earth? I tell you, not at all, but rather division. "For from now on five in one house will be divided: three against two, and two against three. "Father will be divided against son and son against father, mother against daughter and daughter against mother, mother-in-law against her daughter-in-law and daughter-in-law against her mother-in-law" (Luke 12:51-53).

He caused division within the Jewish family Because of those who accepted Him as the Messiah and those who did not. Jesus said, it would be “mother against daughter, father against son (Matt. 10:35). Elijah’s ministry will bring unity to the family as Jesus comes again. He will prepare for Israel’s national salvation by restoring the division in the Jewish family unit this caused the first time. So the first messenger did not restore but Elijah will.

The disciples' confusion was because that they did not yet understand the twofold coming of the Messiah and were still expecting the Kingdom to be set up at that time.

Mark 9:9-13: after they had seen the Elijah of the Old Testament appear with Moses after coming down from the mountain they asked Him, saying, "Why do the scribes say that Elijah must come first?"Then He answered and told them, "Indeed, Elijah is coming first and restores all things. And how is it written concerning the Son of Man, that He must suffer many things and be treated with contempt? "But I say to you that Elijah has also come, and they did to him whatever they wished, as it is written of him." (Mark 9:11-13)

If Elijah had come before the First Coming and restored all things, then all the prophecies of the sufferings of the First Coming would remain unfulfilled. Spiritually speaking, Elijah did come first. John the Baptist did not accomplish the Elijah's ministry of restoration by the First Coming, this is reserved for the Second Coming, not before.

John the baptizer said he was not Elijah and so did Jesus.