The mid part of Nahum 1:3 reads “the Lord hath his way in the whirlwind and in the storm.”

The direct reference to whirlwind here is to the Babylonian army that will come as a whirlwind (Habakkuk 3:14) and as a storm  and carry the Assyrians captive as chaff (Job 21:18). The Assyrians were cruel and afflicting the people of God (Judah), but the Lord has his way in the whirlwind and in the storm suggests that it will be God who is in control of the Babylonian army to destroy the Assyrian kingdom completely. Whirlwinds and storms are natural phenomena that cause destruction (Proverbs 1:27) and as the whirlwind passeth, the wicked is no more; but the righteous is an everlasting foundation (Proverbs 10:25). When the Babylonians captured Assyria and overthrew Nineveh, the Assyrians were utterly cut off (1:15) meaning that they were no more.

Secondarily, the Lord has his way in the whirlwind and in the storm affirms that God is in control of all things, including natural elements. He spoke to Job from a whirlwind  (Job 38:1), and assured that when Job life was tumultuous (like in a storm), he was still in control. Jesus commanded the storm to be calm and they obeyed (Mark 4:39-41).

Points to ponder:
People of God ought not to fret and be dejected, losing hope, when the wicked around them oppress them, for the Lord is in control. In the storms of our life, we can count on Jesus alone, who speaks to us from within the whirlwind and the one whom even the wind and the sea obey. If your life is stormy, call on Jesus, for when he commands the storm, even the great ones, to abate, it will. The Lord (indeed) has his way in the whirlwind and in the storm. 

Nahum 1:3 (KJV)
3 The Lord is slow to anger, and great in power, and will not at all acquit the wicked: the Lord hath his way in the whirlwind and in the storm, and the clouds are the dust of his feet.

Mark 4:37-41 (KJV)
37 And there arose a great storm of wind, and the waves beat into the ship, so that it was now full.
38 And he was in the hinder part of the ship, asleep on a pillow: and they awake him, and say unto him, Master, carest thou not that we perish?
39 And he arose, and rebuked the wind, and said unto the sea, Peace, be still. And the wind ceased, and there was a great calm.
40 And he said unto them, Why are ye so fearful? how is it that ye have no faith?
41 And they feared exceedingly, and said one to another, What manner of man is this, that even the wind and the sea obey him?