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Matthew 3:11 I indeed baptize you with water unto repentance: but he that cometh after me is mightier than I, whose shoes I am not worthy to bear: he shall baptize you with the Holy Spirit, and with fire:

The baptism with the Holy Spirit is a baptism of  blessing and eternal life but that of fire is a baptism of judgment.

The baptism of the Holy Spirit initially took place at Pentecost, as a taste of the powers of the world to come (i.e. the world or age to come is the Kingdom of God on earth) - see Hebrews 6:4,5. The true fulfillment of this verse will come when our Lord returns to bestow the crown of immortal life on all whom he deems worthy. (2 Timothy 4:8).

The judgement by fire is still future and will fall upon all those who have heard the Gospel message and who have been called upon to submit to it but who have rejected it. 

Note the context of this passage. John speaks of judgment as an explanation or exapansion of his words regarding baptism of the Holy Spirit and Fire.  He is speaking of the ultimate granting of eternal life to the faithful and eternal extermination of the wicked. 

Here is the passage in context:

Matthew 3:10-12 Even now the axe is laid to the root of the trees; every tree therefore that does not bear good fruit is cut down and thrown into the fire. 11 "I baptize you with water for repentance, but he who is coming after me is mightier than I, whose sandals I am not worthy to carry; he will baptize you with the Holy Spirit and with fire. 12 His winnowing fork is in his hand, and he will clear his threshing floor and gather his wheat into the granary, but the chaff he will burn with unquenchable fire.

For further reading:

Raised to Judgment:

Resurrection and Judgment: 

After Death, What?

I hope you have found this helpful.

God bless,