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The Pamlico Settlement and the town of Bath were founded during a time of strife.

In 1672, George Fox, founder of the Society of Friends, also known as Quakers, visited Albemarle County, North Carolina. Albemarle County later became the counties of Chowan, Currituck, Pasquotank and Perquimans. He established his church there. The church grew and became engrained in the colony. For several decades, it was the only organized religion in the colony. In 1694, the Quaker church dominated all areas of government with the appointment of John Archdale, a Quaker, as governor. Colonists who were Anglican or Church of England felt discriminated against.

In 1699, a new governor was appointed. Henderson Walker, a zealous Church of England man, was the new governor. In 1700, he persuaded the Assembly to pass a vestry act identifying the Church of England as the official church of North Carolina. This allowed for taxes to pay for the church. Around the same time, Queen Anne ascended the throne, requiring all officials to swear oaths of loyalty to the new monarch. The Quakers, because of their faith, would not make an oath and the affirmations as they had done in the past were rejected by those in authority. This split the colony between the church party and the Quaker party.

Thomas Cary was appointed governor in 1705. He was a well-known South Carolinian who immediately showed a preference for the church party. This preference caused the Quakers to send Emanuel Low to England to effectively remove Cary from office. Low succeeded, but when he returned, Cary was in South Carolina and William Glover was acting in his place. Since it appeared that Cary was a better choice than Glover to the Quakers, Low refrained from showing the document removing Cary from office. Cary switched allegiances in 1708 and with Quaker backing ousted Glover from office. Glover, with ardent church party supporters, fled to Virginia. Cary and the Quakers assumed power through 1710.

In Jan 1711, Edward Hyde arrived from England as governor of the colony. While his commission wasn't technically perfect, at first Cary and others welcomed him and assisted him in taking office. However, when he started pursuing interests contrary to the Quakers, Cary refused to let him stay as governor claiming that until Hyde showed his commission, he was not governor of the colony.

After years of political strife, this resulted in an armed rebellion. Because Cary maintained his home on the Pamlico and was an original grant holder in the city of Bath, it was sometimes referred to as the "seat of government" during his governorship. Many Bath County residents were his supporters. Governor Hyde declared Cary in open rebellion and took steps to seize him by force.

Hyde assembled a force of 80 men under arms, a force he considered sufficient, at his home on Salmon Creek in present-day Bertie County. On 27 May 1711, he crossed Albemarle Sound and entered the Roanoke River where he met with 70 more men under arms. After a two-day march, Hyde's forces arrived at Cary's home only to find that he had fled to Colonel Daniel's home. On 29 May, Hyde with his forces approached Daniels' home which had been fortified with five cannons and had about 40 well-armed men. Hyde found Daniels' place too strong to storm and, being unable to persuade him to surrender, left the field. This heartened Cary's supporters.

Cary now declared himself the true governor and outfitted a brigatine of six guns and several smaller vessels. On 30 Jun 1711, Cary with his ships began an attack on Hyde and his council at the home of Thomas Pollock. Hyde only had 60 men under arms and two cannons. When the brigatine approached shore, one of the shore cannons fired, severing the mast. Cary's crew cut the anchor and sailed away. Hyde sent a crew out on a sloop to pursue the brigatine and when they reached the Sound, they found the brigatine beached with only three crewmen aboard, the rest having made quick departure. Hyde seized the brigatine and all the guns and ammunition on board.

Despite the loss, Cary found some assistance from a recent arrival from England named Richard Roach. With Roach's help, Cary fortified an island in the Pamlico. Cary began to gather and arm an army. Hyde made another unsuccessful attempt to drive Cary out.

Governor Anthony Spotswood from Virginia decided to help out Hyde. Virginia's militia was prepared to march into Carolina. A company of royal marines were dispatched from Chesapeake Bay in mid-July 1711. The Virginia militia never set foot in North Carolina. When Cary's followers saw the marines, they surrendered. It was one thing to challenge Hyde's authority, it was another to commit treason. Cary and his chief lieutenants fled their homes on the Pamlico for Virginia where they were captured and returned to England in chains. Friends helped secure Cary's release. Cary then returned to South Carolina and faded into obscurity.

From 1708 until Cary was overthrown the government had ceased to function. The colonists along the Pamlico River didn't see anything by strife. Because of the constant state of rebellion, crops weren't harvested, if they were planted. In 1711, on top of the strife, there was a severe drought in the area and harvest yields were severely depressed. In the midst of all of this, a yellow fever epidemic struct in 1711 and again in 1712.