From the first paragraph of Scripture, the Holy Spirit was there with the Father and Son creating the world: “In the beginning, God created the heavens and the earth. The earth was without form and void, and darkness was over the face of the deep. And the Spirit of God was hovering over the face of the waters” (Genesis 1:1-2). Derek Kidner provides a helpful observation:
“In the Old Testament the Spirit is a term for God’s outgoing energy, creative and sustaining. Any impression of Olympian detachment which the rest of the chapter might have conveyed is forestalled by the simile of the mother-bird ‘hovering’ or fluttering over her brood.”
Notice then the regenerating work of the Holy Spirit in our salvation. In John 3, when Nicodemus approaches Jesus at night to inquire more about His ministry, Jesus took the opportunity to bring in how one is “born again.” Jesus uses the terms “born again” and “born of the Spirit” synonymously, but the latter certainly clarifies.
Jesus answered him, “Truly, truly, I say to you, unless one is born again he cannot see the kingdom of God.” Nicodemus said to him, “How can a man be born when he is old? Can he enter a second time into his mother's womb and be born?” Jesus answered, “Truly, truly, I say to you, unless one is born of water and the Spirit, he cannot enter the kingdom of God. That which is born of the flesh is flesh, and that which is born of the Spirit is spirit. Do not marvel that I said to you, ‘You must be born again.’ The wind blows where it wishes, and you hear its sound, but you do not know where it comes from or where it goes. So it is with everyone who is born of the Spirit.”
Just as the Holy Spirit was present when everything was born, hovering over the waters, so too is the Spirit present to make us born again. By Jesus saying, “Born of the Spirit,” this clarifies the nature of the transformation. One is not born again out of their internal will or desire but from the outward, heavenly work of the Holy Spirit, who reveals God and His Word to humanity. The apostle John sets the table in the prologue of his gospel by saying, “But to all who did receive him, who believed in his name, he gave the right to become children of God, who were born, not of blood nor of the will of the flesh nor of the will of man, but of God” (John 1:12-13). God the Father, through His Son, by the power of the Spirit, regenerates His people to bring them into His fold.