The short answer? Murder.
The long answer? Virginia in 1670 was made up of three groups: rich whites, poor whites, and Native Americans (African slaves, a forth group, were not yet present in significant numbers…see below).
If you were a poor white (and had survived your initial 5-year indenture contract) you basically had two options for a livelihood: continue working for (low) wages as a hired servant for a rich landowner, or venture into the western frontier to start your own plantation. If you did the latter, you risked being attacked by the Native Americans, who would interpret your move as encroachment on their land.
Because of this, many poor whites wanted to raise a militia to attack the Native Americans and push them further west so they could create their own tobacco farms. The rich whites (who were in control of the government and commended the militia) didn't want this, as even if they won against the Natives (not a given) the end result would be new tobacco farms that would be in direct competition to the farms those rich whites already owned.
This division between rich and poor simmered until Nathaniel Bacon took matters into his own hands, creating his OWN militia and attacking the Native Americans without official government permission. His military killed so many Natives that the rest fled the region. Governor Berkeley protested this, so in response, Bacon attacked Berkeley himself by invading Jamestown and burning it down. Berkeley and his allies retreated to an English warship in the harbor.
Things may have gotten worse except Bacon died of dysentery soon afterward (the "bloody flux" as it was known), which seems random now but was a pretty common at the time. Without Bacon's leadership his militia broke into pockets and many went home. Later, official military troops arrived from England and helped the government hunt down the few who continued to resist, which took a couple years.
When it was all over Berkeley was fired from his post by the King and the colony became more directly under royal control. Another effect was a sharp subsequent increase in African Slaves. After the rebellion, rich white people worried that importing more white indentured servants into the colony would create another Bacon's Rebellion situation, so they started buying African slaves instead (who theoretically stay slave workers forever). Whether Bacon's rebellion caused this switch from English to African labor or simply accelerated a change that was already underway is currently in debate among professional historians.