Not sure what you read, but it seems to be getting some facts confused. In the 1500s, there were many different Native nations throughout North America. No individual nation would have had a population of 28 million. Contact-era populations for individual nations were often in the 10s of thousands. If the Plaquemine culture was as unified as Natchez oral history would indicate and the historical record hints at, they might have had a population in the 100s of thousands. Once we get down into Mesoamerica (which is also part of North America, but often gets separated out in these sorts of discussions) then populations of the individual nations skyrockets - the city of Tenochtitlan alone had a population of 200+ thousand people in the early 1500s. Adding up the local population estimates gets population estimate for the entirety of the Americas ranging from 50 million to 100 million.

The figure of 90% population loss is derived from an overapplication of numbers drawn from early colonial Latin America censuses. While disease played a role in that population loss, it was just one factor in many including war, harsh working conditions, etc., that occurred over many years. In other areas, the specific percentage of population loss varies by regional and what specific event(s) you're considering.

So when we're talking about "a mysterious plague around 1600", I'm going to have to assume what we're talking about is the epidemic in the mid-1610s that inflicted heavy losses in southern New England. These losses were heaviest in eastern Massachusetts, where some Wampanoag communities were completely wiped out and the over all loss of life for the Wampanoag might have been in the 90% range. The epidemic hit the neighboring Narragansett in Rhode Island as well, but not has heavily; fearful that the Narrangansett would take advantage of their weakness, the Wampanoag allied with the English in 1620 and aided the colonists in establishing the Plymouth colony. The Pequots in Connecticut were barely affected by the epidemic at all and retained a population of some 16,000. The identity of the disease that caused this epidemic is currently unknown, though we can say with relatively certainty that it wasn't smallpox. Since English slavers had recently been making forays against Native peoples in the area (which is why Tisquantum - better known as Squanto - had been across the Atlantic six times before the Pilgrims reached Plymouth), they may have introduced another European disease into the area.

Epidemics like this and the later smallpox epidemic in 1633 did facilitate European expansion into the area - to the point that some colonists believed that God was clearing the way for them. As I mentioned, the population loss encouraged new alliances with Europeans that gave the English a foothold in the area. The sustained losses and the difficulty of rebuilding the population in the face of successive waves of epidemic (while simultaneously additional colonial immigrants arrived from England) shifted the balance of military power in the long run.