וְר֣וּחַ אֱלֹהִ֔ים מְרַחֶ֖פֶת
Then God's Spirit moved
The raw ingredients were gathered into place. The rules were laid down. It was time to build a universe.
When the Spirit (ר֣וּחַ) of God moves, things happen. There is no stopping Him. The word for spirit is descriptive, for the same word in both Hebrew and Greek is translated wind, breath and "spirit". In this context, the breath of God personifies the general work God does by moving air as great winds. In some way, God is working directly in miraculous ways that defy the very laws of nature so recently established.
As the Spirit moved over, through and around the scattered chaos, the force of gravity began to form a huge sphere. The crush would bring neucleai together where the strong and weak forces would allow atoms to be formed. Something big was in the works in a "miniature", comparatively speaking, universe was formed in a most compact form.