You have wearied the LORD with your words. “How have we wearied him?” you ask. By saying, “All who do evil are good in the eyes of the LORD, and he is pleased with them” or “Where is the God of justice?” [3.1] “I will send my messenger, who will prepare the way before me. Then suddenly the Lord you are seeking will come to his temple; the messenger of the covenant, whom you desire, will come,” says the LORD Almighty.  But who can endure the day of his coming? Who can stand when he appears? For he will be like a refiner’s fire or a launderer’s soap.  He will sit as a refiner and purifier of silver; he will purify the Levites and refine them like gold and silver. Then the LORD will have men who will bring offerings in righteousness.
COMMENTARY: In finishing up chapter two, Calvin fixates on the logic at work in the imagined responses on the part of the Jewish leadership to the criticisms made by Malachi. They claim that either God approves of those who do evil—i.e., those who afflict the Jewish people and that Malachi claims as agents of divine judgment—or that God is absent. Furthermore, Calvin understands them to imply by this charge of God’s absence that God in fact does not exist: “they intimate that there is no God, for he cannot exist without exercising judgment” (563). Calvin follows up with this a few pages later, giving the Jewish leaders some credit for this line of thinking insofar as it is true “that there is no God, except he be the judge of the world; for he cannot divest himself of his office without denying himself” (566). This language of “office” puts me in mind of the munus triplex - the threefold designation of Christ’s office as “prophet,” “priest,” and “king” that was central to Calvin’s christology and became something of a defining feature of Reformed theology. In Calvin, then, we get a very close identification between God (and Christ’s) being and God’s (and Christ’s) roles, or tasks, or functions, so much so that these functions become the expressions of God’s being to such an extent that to deny the function is to deny the being.
But, of course, God has not ceased to function as the world’s judge, and so God has not ceased to exist. On Calvin’s reading, the Jewish leaders imagined here make the regrettable mistake of thinking that just because God isn’t seen to punish their enemies, it means that God has ceased to act as judge. In fact, Calvin reads Malachi as asserting that God maintains God’s office of judge precisely by judging these Jewish leaders. So Calvin concludes this line of thought by saying: “We hence learn that they did not complain through zeal for what was right, but because they would have God bound to them to undertake their cause like earthly patrons” (565). Of course, this mistake continues to be frequently made even in our own time.
Calvin’s comments on the first verses of chapter three have failed to inspire me. Suffice it to say that Calvin understands the “messenger” in verse 1 as Jesus (via a connection to David, who is a “type” of Christ ), he reads Malachi as speaking ironically in suggesting that the Jewish leaders desire his arrival , he conceptualizes the distinction between the godly and the ungodly both in terms of the former desiring Christ’s coming  and in terms of the former being purified by the fire of God’s judgment while the latter are simply consumed .
(Calvin concludes each of his lectures on Malachi with a prayer.)
Grant, Almighty God, that since we are by nature so prone to rash judgment, we may learn to submit to thee, and so quietly to acquiesce in thy judgments, that we may patiently bear whatever chastisements thou mayest daily allot to us, and not doubt but that all is done for our wellbeing, and never murmur against thee, but give thee the glory in all our adversities; and may we so labour to mortify our flesh, that by denying ourselves we may ever avow thee to be the only true God, and a just avenger, and our Father, and that thus renouncing ourselves, we may yet never depart from the purity of thy word, and be thus retained under thy yoke, until we shall at length attain that liberty which has been procured for us by thine only-begotten Son. – Amen.