How Does the Spirit Work?

In what manner does the Holy Spirit operate in individual hearts?

It does not appear, that any specific and certain rule can be laid down. The methods of the divine operation appear to be one of the secret things, which are hidden with God. Accordingly the Holy Spirit, so far as his method or manner of his influences is concerned, operates differently in different cases. "The wind bloweth where it listeth, and thou hearest the sound thereof, but canst not tell, whence it cometh, and whither it goeth. So is every one that is born of the Spirit."  He sometimes comes with sudden and almost visible efficacy, and produces his results with "observation." But still more frequently, as it seems to us, he comes as a "still small voice," and operates in a secret and silent manner; but with no diminution of effective power and of inward purification.

Says Mr. Fletcher:

If the Lord be pleased to come softly to thy help; if he make an end of thy corruption by helping thee gently to sink to unknown depths of meekness; if he drown the indwelling man of sin, by baptizing, by plunging him into an abyss of humility; do not find fault with the simplicity of his method, the plainness of his appearing, and the commonness of his prescription. Nature, like Naaman, is full of prejudices. She expects that Christ will come to make her clean with as much ado, pomp, and bustle, as the Syrian general looked for when he was wroth and said, 'Behold, I thought he will surely come out to me and stand and call on his God and strike his hand over the place and recover the leper.' Christ frequently goes a much plainer way to work and by this means he disconcerts all our preconceived notions and schemes of deliverance. 'Learn of me to be meek and lowly of heart, and thou shalt find rest to thy soul.' Instead therefore of going away from a plain Jesus in a rage, welcome him in his lowest appearance, and be persuaded that he can as easily make an end of thy sin, by gently coming in 'a still small voice,' as by rushing in upon thee in a 'storm, a fire, or an earthquake.' [John Fletcher's Works, Vol. II, p. 650.] 

— edited from The Interior or Hidden Life (2nd Edition, 1844) Part 3, Chapter 1.