The Neo-Universe is the recreation of the First Universe. After the First Universe was destroyed by the Cataclysm, God moved through both the energies of the explosion and the will of The B-Team to recreate the universe in its present form (relative to the plot). This included fully developed Species all over the universe, but Earth was of particular interest to both God and the B-Team. The planet was almost exactly as it was before the Cataclysm, but the Human race appeared in numbers in the thousands and were without a civilization. Following the scientific data that they found in The Book of Epic, they reconstructed a civilization, which made it to relatively modern levels in a very short period of time.
The B-Team and Vyrna are the only remnants of the First Universe to make it to the Neo-Universe. Everything else, all of the planets, galaxies, species, and civilizations, are completely newly created through the power of God. However, though the power of God created the Neo-Universe, it was not a complete "recreation;" things are still in a fallen state, as there are hostile species and death still present. The Human race, too, is fallen; they quickly divided and began warring amongst themselves.