I believe Gen 1:2 points to a time before the earth was a water world about 4.5 billion years ago. The deep is the magma core and mantle and as the earth cooled the surface solidified and shrouded the light from within and the surface then became dark (besides light from sun) and void, similar to how the moon looks now.
Then God hovered over the deep and faced down the darkness. This was when Theia impacts Earth and forms the moon.
Day 1 then begins about 4.4 billion years ago, with God saying let light be!
It is then after this that late heavy bombardment turns earth into a water world about 4.1 to 3.8 billion years ago. Day 2 begins when God starts forming the earths crust (firmament). Here is an interesting article on the late heavy bombardment: