We are told in Genesis 1.2 that the Spirit of God took a specific place before illuminating, shaping, and filling 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.

The Hebrew words for “without form and void” and “hovering” only occur one other place in the Pentateuch. Here is Deuteronomy 32.10, 11 in some context:

Remember the days of old;
consider the years of many generations;
ask your father, and he will show you,
your elders, and they will tell you.
When the Most High gave to the nations their inheritance,
when he divided mankind,
he fixed the borders of the peoples
according to the number of the sons of God.
But the Lord’s portion is his people,
Jacob his allotted heritage.

He found him in a desert land,
and in the howling waste of the wilderness;
he encircled him, he cared for him,
he kept him as the apple of his eye.
Like an eagle that stirs up its nest,
that flutters over its young,
spreading out its wings, catching them,
bearing them on its pinions,
the Lord alone guided him,
no foreign god was with him.
He made him ride on the high places of the land,
and he ate the produce of the field,
and he suckled him with honey out of the rock,
and oil out of the flinty rock.

Moses is describing how God led Israel through the wilderness.  The text has shown us that God did so leading them by a pillar of cloud by day and a pillar of fire by night. That cloud stationed itself on Mount Sinai. Moses went up into it to receive the Ten Commandments from God. The cloud moved into the Tabernacle with great fire and glory (Exodus 40).  Moses compares God’s actions to that of an eagle but he is also appealing back to the original creation.  God flying above Israel in the wilderness in a cloud is like the Spirit hovering over the original chaos of creation in order to bring new light and life.

This opens up a lot of significance to the reader. For example, one sees that, when Pharaoh and his army pursued Israel at the Red Sea, the cloud came between them, bringing light to Israel and darkness to the Egyptians. Then the waters were moved and new dry land appeared.  This is a powerful reminder of the first and third days of creation and designate Israel, in its founding, as a new creation.  Thus Isaiah explains that Israel is a kind of new creation:

I am the LORD your God,
who stirs up the sea so that its waves roar—
the LORD of hosts is his name.
And I have put my words in your mouth
and covered you in the shadow of my hand,
establishing the heavens
and laying the foundations of the earth,
and saying to Zion, “You are my people” (51.15, 16).

It also clearly establishes that the Glory Cloud that led Israel through the wilderness and that moved into the Tabernacle (and later Solomon’s temple) is especially a manifestation of God’s Spirit.

When Israel returns from Babylon to rebuild the Temple, many are overwhelmed with sadness about it:

And all the people shouted with a great shout when they praised the Lord, because the foundation of the house of the LORD was laid. But many of the priests and Levites and heads of fathers’ houses, old men who had seen the first house, wept with a loud voice when they saw the foundation of this house being laid, though many shouted aloud for joy, so that the people could not distinguish the sound of the joyful shout from the sound of the people’s weeping, for the people shouted with a great shout, and the sound was heard far away (Ezra 3. 11-13).

This led to discouragement and, for awhile, the exiles gave up on rebuilding the Temple. The prophet Haggai was sent to rebuke them for this, and to encourage them that, even though small, the Temple was important.

Speak now to Zerubbabel the son of Shealtiel, governor of Judah, and to Joshua the son of Jehozadak, the high priest, and to all the remnant of the people, and say, “Who is left among you who saw this house in its former glory? How do you see it now? Is it not as nothing in your eyes? Yet now be strong, O Zerubbabel, declares the Lord. Be strong, O Joshua, son of Jehozadak, the high priest. Be strong, all you people of the land, declares the Lord. Work, for I am with you, declares the LORD of hosts, according to the covenant that I made with you when you came out of Egypt. My Spirit remains in your midst. Fear not” (2.2-5).

So after Sinai God’s Spirit moved into the Tabernacle so that God could dwell among his people, and God is telling the people that he also dwells in the Temple they are making even though it isn’t as visibly glorious as Solomon’s was. The same Spirit that hovered over the waters at the original creation was with the exiles to re-create them.