It never happened, there weren't 100 million, even the largest civilizations like the Aztecs, Maya and Incas only had a few million each. In north America there were just a few 100k hunter gatherers and some native farmers collected in the few places suited to their style of agriculture scattered across the continent, entire areas were completely unpopulated and those that were were only seasonally migrated through.

Jamestown starved because it was composed of middle class religious fanatics who didn't know how to farm. Once actual farmers started to migrate to the Americas they had no trouble producing food and bred like rabbits, rapidly outnumbering the natives. Puritans would enter new land thinking it is empty, spend 9 months there, then once season the natives would arrive, maybe only a dozen, 2 or 3 families there to hunt the wild game and move on who were barely affected by the fields raised by the Europeans. Whatever minute reduction in wild game it caused was offset by trade for European iron tools and manufactured textiles.

The killing began as a result of war, which could have been caused by either side, but the natives, not being sedentary peoples with strict laid out laws, often had warriors acting on their own to raid Europeans to collect their iron, whereas it was difficult for European criminals to wander out into the wilderness to steal the furs and tobacco of the natives. A raid would lead to Europeans seeking out the raiders, destroying a village in the process, leading to an escalation and war, in which the Europeans usually won due to greater numbers. European settlers would eagerly move into the cleared area and closer to the frontier and native raids and the process would repeat.