John the Baptist is at the Jordan river preaching repentance and offering baptism to those in Jerusalem, Judea and the surrounding area who came to hear him (Matthew 3:5). Although some came out of a sincere desire to hear the truth, others came for selfish reasons (verse 7 - 8).
John's response to the self-righteous religious leaders who came to hear him was to mention a baptism of fire that will be carried out by Jesus Christ.
John stated that Jesus would soon, ". . . baptize you with the Holy Spirit, and with fire" (Matthew 3:11, HBFV). Notice that two baptisms are mentioned. The first one occurs when someone repents of their sins, accepts Christ as their Savior, and they receive God's Spirit which makes them a true Christian. Although most religious leaders were initially against the gospel some of them later repented (Acts 6:7). The second baptism, however, is employed as a penalty.
John's continues his discussion by scolding and warning the leaders of what will happen to those who refuse to repent. Using symbolic language, he warns that those who are considered "chaff" will receive a unique baptism not of water but of fire! Verse 12 of Matthew 3 states, "Whose winnowing shovel is in His hand, and He will thoroughly purge His floor, and will gather His wheat into the granary; but the chaff He will burn up with unquenchable fire."
Verse 12 of Matthew 3 uses the same dual comparison as verse 11. Jesus will first collect HIS wheat and put it into his granary, which corresponds to the "good" baptism of verse 11. The chaff, however, corresponds to the second group of people who will be burnt up in unquenchable fire. How can we, however, verify that this is a correction interpretation?
In Matthew 13 Jesus gave a parable about a man who discovered his enemy had secretly planted weeds among his good wheat seeds. When the man's servants asked him what should be done he states, "Allow both to grow together until the harvest . . . (then) gather the tares first, and bind them into bundles to burn them; but gather the wheat into my granary." (Matthew 13:30).
Jesus interprets his parable of Matthew 13:24 - 30 for us a few verses later when he states the wheat or good seed symbolizes those who will ultimately be in God's kingdom (verses 37 - 38). The tares (weeds), however, are the unrepentant who will be receive a baptism of fire - meaning they will soon be burned up (verses 38, 40).
Some professing Christians who think that a baptism of or by fire is a good thing believe 'the floor' mentioned by John the Baptist in Matthew 3:12 represents individual Christians who have their sins burned away or purged. Jesus, according to this belief, uses his 'fan' or 'winnowing shovel' to stoke up flames meant to purge a believer's "chaff" or "dross" (their sins) out of their lives and leaving only "the wheat" or good part. This interpretation, however, is simply not correct.
Notice that the "fan" in the hand of Jesus is used to remove CHAFF from his floor. The wheat that remains he gathers up for his granary. What John preached in Matthew 3 and the parable Jesus gave in Matthew 13 OVERLAP regarding how God will ultimately judge humans by one of two baptisms.
The wheat of both Matthew 3:12 and Jesus' parable in Matthew 13 represent true Christians. The chaff (Matthew 3:12) or tares (13:25 - 30) are unrepentant people deceived by Satan the devil. They, for a time, are allowed to exist alongside the righteous. When the moment of God's judgment comes, he will separate the wheat (righteous) from the chaff or tares (those who refuse to repent). The righteous will be allowed entrance into God's Kingdom.
What will happen to the chaff or tares? They will receive a baptism of fire, meaning that they will be burnt up and destroyed forever in a lake filled with it (Revelation 20:14, Malachi 4:1)! It is definetly something a person should not desire!