Matthew 3 begins with a description of John the Baptist, who is baptizing people in the Jordan river.  The relevant passage for us begins:

[7] But seeing many of the Pharisees and Sadducees were coming upon his baptism, he said to them: “Brood of vipers, who showed to you to flee from the coming wrath? [8] Therefore make fruit worthy of repentance [9] and do not think to say to yourselves ‘We have Abraham for our father.’ For I say to you that God is able to raise children of Abraham from these stones. [10] But already the ax lies against the root of the trees. Therefore every tree not making good fruit shall be chopped down and cast into the fire. 

[11] But I baptize you in water unto repentance, but the one coming after me is stronger than me, for whom I am not worthy to carry his sandals.  This one shall baptize you in the holy spirit and fire. [12] For whom the winnowing shovel is in his hand, and he will thoroughly purge his threshing floor and gather together his wheat unto the granary, but the chaff shall be consumed in unquenched fire. 

Here it seems quite possible to read this passage with the basic understanding of “two-thirds will be destroyed, one-third will be purified by fire,” and that this understanding is particularly directed at the Pharisees and Sadducees (or perhaps Jews more broadly), in explicit contrast to Christians, who presumably are the trees producing fruit worthy of repentance.  

As always, it is also useful to compare Matthew to the parallel passage in Mark 1.7-8:

[7] And he proclaims saying: the one who comes after me is stronger than me, for who I am not worthy of stooping to loosen the thongs of his sandals. [8] I baptize you in water, but this one shall baptize you in the holy spirit.

Obviously this is quite brief compared to Matthew, and entirely omits any language of fire.  It should be remembered that of the Gospels, Mark’s is the one most plausibly composed before the destruction of Jerusalem and the Temple at the hands of the Romans.  Between the composition of Mark and the composition of Matthew, substantial elaboration has been made on this passage, as well as the explicit insertion of apocalyptic language.  As we shall see, the parallel passage in Luke 3:7-17 shares a great deal of this language:

[7] Then he says to the crowds who went out to be baptized by him: Brood of vipers, who showed you to flee the coming wrath? [8] Therefore make fruits worthy of repentance and do not begin to say among yourselves, we have Abraham for a father.  For I say to you that God is able to raise children of Abraham from these stones. [9] Already the ax lies against the roots of the trees, therefore every tree not making good fruit shall be chopped down and cast into the fire.

[10] And the crowd asked him, saying: What therefore should we do? [11] And responding he says to them: who has two cloaks should transfer to someone lacking, and who has food likewise should do. [12] And the tax farmers also came to be baptized by him, and they said to him: Teacher, what should we do? [13] And he said to them: Extract nothing besides what has been commanded to you. [14] And soldiers asked him, saying: What should we also do? And he said to them: Do not harass anyone nor falsely accuse them and let your wages suffice you. 

[15] And while the people were awaiting and while they all argued in their heart around John, whether the man was the christ, [16] John responded to all saying: I baptize you with water. But the one who comes is stronger than me, for whom I am not sufficient to loosen the thongs of his sandals. This one shall baptize you in the holy spirit and fire. [17] For whom the winnowing shovel is in his hand, and he will thoroughly purge his threshing floor and gather together his wheat unto the granary, but the chaff shall be consumed in unquenched fire.

As we have discussed elsewhere, it is commonly accepted that Mark was the Gospel that was composed first, and it was used as a source for both Matthew and Luke.  Here, however, we see evidence for the Q source, which is believed to be a collection of the sayings of Jesus that was used as a source for both Matthew and Luke, but for which no manuscripts survive. 

Luke places these passages within a context that universalizes them: the “brood of vipers” is the whole crowd, and vv. 10-14 in Luke outline godly behavior to avoid the coming wrath. In Luke, this passage serves as a general rebuke to the ungodly and call to piety in a fairly broad sense, which is consistent with Luke’s greater focus of Christianity for gentiles. Matthew, on the other hand, has Jewish Christian priorities, which is to say that a major argument made throughout Matthew is that in the wake of the destruction of the Temple, it is Christianity that is the proper heir to the Hebrew tradition, rather than the Pharisees or Sadducees.  So here we see that it is these latter groups who are the brood of vipers. Within this context, Matthew’s fondness for Zechariah and its bad shepherd imagery makes quite a bit of sense. 

When it comes to the fire imagery here, I think it is also worth keeping in mind the framework of “two parts will perish, one part will be purified in fire,” because there are actually two separate fire metaphors here.  In the first, trees producing bad fruit are chopped down and thrown into the fire, which I think corresponds to the two parts that will perish.  But I think when we read about chaff being burned, this corresponds to the remnant third be purified with fire.  Wheat and chaff were originally a unified whole, and so the wheat indicates the purified remnant and the chaff the impurities which were burned away