Genesis 1:2 (Spirit of God)
The earth was formless and void
  These two words, “formless” and “void”, point to an outline of God’s creative work during the next six days and beyond. The first three days of creation God brought form to the formless, while the next three days He filled the void. More specifically, on each of the first three days God performed acts of separation to make a distinction between one thing and another. On the fourth day He populated the structure that He created on the first day, on the fifth day He populated the structure from the second day, and on the sixth day He populated the structure of the third day.
| Formed | Filled |
| 1. Light/Darkness | 4. Sun, Moon, Stars |
| 2. Heavens/Earth (Waters above/below) | 5. Birds & Fish |
| 3. Seas/Dry Land | 6. Land animals, Humans |
 Note the relationship between God’s acts of forming and those of filling. He first formed and then He filled. And what He filled was precisely the structure which He had formed. He made the sun and moon to fill the heavens and earth with light. He commanded the birds to fill the skies, the fish to fill the seas, and He commanded man to fill the earth and subdue it.
He is the God who formed the earth and made it,
He established it and did not create it a waste place,
But formed it to be inhabited. — Isa 45:18, [emphasis added]
 This “forming and filling” is also a broad summary of God’s work through the remainder of redemptive history. The Creator forms and then fills. God’s acts of “forming” were works of separation, and the Old Testament is a book of separation in many ways. God made a distinction between the sacrifice of Cain versus that of Abel. He separated Noah from His generation, He separated the nations in Genesis 11, He took Abram out of His land to make from Him a separate and distinct people. Later God made a separation between Isaac and Ishmael, and between Jacob and Esau. He put a separation between the Hebrews and the Egyptians. He sent down instructions for a tabernacle to separate the camp of Israel from the Holy Place, and for a veil to separate the Holy Place from the Most Holy Place. Through Moses God sent the Law, and again the Law is largely about separations and distinctions. The Law separates good from evil, the holy from the common, the clean from the unclean, justice from injustice, and life from death.
 However, the Law has no power to fill up or the good categories that it delineates. The Law shows what is good, what is holy, what is clean, what is just, and what is the way of life, but the Law has no power to “inhabit” those categories. The New Testament is largely a book of the filling that comes in and through Jesus Christ.
He who descended is Himself also He who ascended far above all the heavens, so that He might fill all things. -Â Eph 4:10
The structure which Jesus fills is precisely the form which God had prepared in advance through Moses.
“Do not think that I came to abolish the Law or the Prophets; I did not come to abolish, but to fulfill.” Matt 5:17
For the Law was given through Moses; grace and truth were realized through Jesus Christ. - John 1:17
 Jesus was filled with the Spirit of God, and after His ascension Christ sent the Holy Spirit to fill His church in accordance with the prophecy of Joel. By His Spirit we are filled with joy, filled with the fruit of righteousness, and filled with empowerment to be Christ’s witnesses. New Testament Christianity all about fullness in Christ:
For this reason I bow my knees before the Father…, that He may grant you… to know the love of Christ which surpasses knowledge, that you may be filled up to all the fullness of God. - Eph 3:14-19
Darkness was over the surface of the deep
 We’ll look more at the Light in verses 3-5. For now suffice it to observe that apart from the Word of the God there is only darkness.
… the face of the waters
 First of all, one might ask, “What waters? The Spirit of God was hovering over the face of what waters? There wasn’t any mention of waters up to this point.” Some commentators resolve this by saying that the formless, void, darkened waters were created in verse one. But that leads to the question: did God say, “Let there be waters,” before He said, “Let there be light”? I have taken the stance that verse one is in fact a heading and that there weren’t any acts of creation before God said, “Let there be light.” So then, what are these waters and where do they come from?
 There are some more clues about the nature of the waters in the rest of the chapter. On the second day God created an expanse to separate the waters below from the waters above. The earth was formed out of the waters below (cf. II Peter 3:5) and these waters were gathered into the seas on the third day. Looking at the fourth and fifth day we see that not only did birds fly in the expanse separating the waters, but indeed the sun, moon, and stars were placed in that expanse. That indicates to me that the “waters above” were beyond the stars, and indeed still are (Ps 148:1-4). We know what became of the waters below, but we need to know more about the waters above in order to put the pieces together.
  The Old Testament provides more clues, but ultimately it is only in the New Testament that we can look beyond the shadows to ultimate reality. Revelation is a companion book to Genesis in that Genesis is a book of beginnings and Revelation is a book of endings and new beginnings. It seems to me that all of the themes and storylines that open up in Genesis only attain their completion and resolution in Revelation. It has also been my observation that the closer something appears towards the front of Genesis, the further back you in Revelation, as in a mirror, you should look to find what ultimately becomes of it. So to understand the “waters” that mysteriously appear in the first chapter of the Bible, I ultimately look to the last chapter of the Bible.
Then he showed me a river of the water of life, clear as crystal, coming from the throne of God and of the Lamb, in the middle of its street. On either side of the river was the tree of life, bearing twelve kinds of fruit, yielding its fruit every month; and the leaves of the tree were for the healing of the nations. - Rev 22:1-2
 God Himself is a fountain of living water (Jer 2:13, Jer 17:13). Thus I believe that the river of living water that will forever flow from the throne of God and of the Lamb has already been flowing for a very long time — at least as far back as “the beginning.” The ancient prophets had brief glimpses of this river (Ps 36:8-8, Ps 46:4, Ezek 47:1-9), but among men the apostle John received the clearest vision of all.
  Now, we are told that “living water” is a Hebrew idiom which simply means “moving water” or “running water.” OK, fair enough. But I’m convinced that there is more to the Biblical meaning than that.
“It will come about that every living creature which swarms in every place where the river goes, will live. And there will be very many fish, for these waters go there and the others become fresh; so everything will live where the river goes.” - Ezek 47:9
The living water that flows from the throne of God and the Lamb is called living water because it truly has the power to bring life wherever it goes. All life sprung from these waters in the beginning, and all life will be sustained by them in eternity future.
The Spirit of God was hovering over the face of the waters
  Now back to Genesis 1:2, where we see the Spirit of God hovering over the face of the waters. The very mention of the “Spirit of God,” rather than simply “God” is another early hint of the One God’s plural nature within His singular divine self. Interestingly, the “Spirit of God” is not mentioned again specifically until Exodus 31:3 when the Lord filled Bezalel with the Spirit of God to be empowered for the craftsmanship required for the construction of the tabernacle. Lest anyone think that the Spirit of God only came into existence or only began His work at a later point in history, His preeminent role is mentioned here at the very beginning.
  As with the waters themselves, His presence is enigmatic. What is the Spirit of God doing here? Why is he hovering over the waters? Although many commentators have tried to piece together a full picture based on the scant clues of the chapter, I would again suggest that only looking back from the New Testament do the blurry images of the Old Testament become sharp and focused.
“He who believes in Me, as the Scripture said, “From his innermost being will flow rivers of living water.’” But this He spoke of the Spirit, whom those who believed in Him were to receive; for the Spirit was not yet given, because Jesus was not yet glorified. - John 7:38-39
Thus it was very natural that the Spirit of God was hovering over the waters since He, as one person of the Triune Godhead, is Himself a fountain from which rivers of living water flow.
  There has never been and can never be any life except the which comes by the Spirit (literally “breath”) of God (e.g. Ps 104:30, Ezek 37:9). Likewise there is no real spiritual life apart from drinking from the Fountain of living water Himself:
As the deer pants for the water brooks,
So my soul pants for You, O God.Â
My soul thirsts for God, for the living God
Ps 42:1-2Jesus answered and said to her, “If you knew the gift of God, and who it is who says to you, “Give Me a drink,’ you would have asked Him, and He would have given you living water. … whoever drinks of the water that I will give him shall never thirst; but the water that I will give him will become in him a well of water springing up to eternal life.”
John 4:10-14
 (See also Ps 63:1, Ps 143:6, Isa 41:17-18, and Isa 55:1.) Therefore it is no surprise that the Spirit and the water are mentioned together so many times in Scripture with reference to life, especially the abundant life (e.g. Isa 44:3, Matt 3:11, John 3:5, Acts 1:5, I John 5:6-8).
 As a bird protecting its young, so the Spirit of God has “hovered” or “brooded” over the waters of life from the beginning of creation (cf. Gen 1:2 with Deut 32:1, Isa 31:5). He has not only been using the waters below to bring forth and sustain life, He has also been guarding and dispensing the waters above to strengthen the parched voice of Christ’s bride as she cries out, together with the Spirit, “Come, Lord Jesus!”
The Spirit and the bride say, “Come.” And let the one who hears say, “Come.” And let the one who is thirsty come; let the one who wishes take the water of life without cost. Rev 22:17
Then He said to me, “It is done. I am the Alpha and the Omega, the beginning and the end. I will give to the one who thirsts from the spring of the water of life without cost.” Rev 21:6
 Now we can are prepared to adequately answer the question, “Why was the Spirit of God hovering over the face of the waters at the beginning of creation? What was He doing there?” A satisfactory answer requires the interpretive principle taught, for example, in Romans 15:4, “For whatever was written in earlier times was written for our instruction, so that through perseverance and the encouragement of the Scriptures we might have hope [emphasis added].” The instruction and encouragement for us in Genesis 1:2 is this: if Christ, the Word of God, came to form the first earth and bring life out of the waters as the Spirit of God was quietly hovering over them, then how much more will Christ most certainly come now as the Spirit of God is expectantly calling out to Him across the face of His living waters! More consisely, we can say that Genesis 1:2 is there to tell us, when fused together with Revelation 22 that: yes, Jesus is coming!
Know this first of all, that in the last days mockers will come with their mocking, following after their own lusts, and saying, “Where is the promise of His coming? For ever since the fathers fell asleep, all continues just as it was from the beginning of creation.” For when they maintain this, it escapes their notice that by the word of God the heavens existed long ago and the earth was formed out of water and by water… -2 Peter 3:3-5