As they began to pay attention to the corruption pervading the English government, John Winthrop and his fellow Puritans got swept up in events happening far from Winthrop's Groton estate. The Puritan movement found itself in a position where it thought it stood as the last line of defense against the wickedness of English culture. While their preachers condemned the corruption from the pulpit, it was left to the laymen to save England where they could. Winthrop and other Puritans who served as justices began enforcing increasingly strict interpretations of the law to punish wrongdoers who came in front of the court. Likewise, Puritan members of Parliament–who were at least a loud minority if not an outright majority–began passing harsh laws to try and clean up society; Winthrop himself helped to draft a bill against drunkenness in the late 1620s. Parliament had made progress under Queen Elizabeth I establishing itself as a legitimate means of governance, progress which had been continued under Elizabeth's successor, James I.

However the entire situation began to change for the worse in 1625 when James I died and was replaced by by his son, Charles I. When Parliament, which controlled fiscal policy in England, refused to grant Charles the money he demanded to run his programs, he dissolved the body. When it later reconvened, an Anglican bishop began the session with a sermon on obedience and service to one's king. However, the new Parliament was hardly more cooperative than the last, so Charles sent it home and set about raising money using unconventional means. He announced a mandatory loan for English citizens and went about collecting it just as if Parliament had levied a new tax. Many Puritans, sensing the new king's evil side, refused to pay, and the king's forces arrested two of two of Winthrop's close friends and sent them to jail.

Even more troubling for the Puritans than Charles's new fiscal policies was the sharp change in religious feelings in England. For one, Charles had married a Catholic–opening himself up to charges that he was treating the religion leniently–and he had continued a trend started by James I called Arminianism. Under the new belief, a person could be saved solely through his or her own faith and righteous actions, thereby disavowing the Puritan ideal of predestination. In fact, Charles brought the Arminians back to the pulpits (they had been banned from preaching under Elizabeth) to voice support for his new spending and to preach obedience to the king. Those in the Anglican Church who opposed the king's moves quickly found themselves removed from power and replaced by Arminians.

Parliament tried to fight back, demanding an end to the unfair regal taxation and an end to the heresy spreading in the church. It passed a resolution stating that anyone who preached Arminianism should be considered an enemy of the state, but Charles remained more powerful than the members of Parliament. He dissolved the body for a second time and made it clear that there would be no third Parliament.

Winthrop knew that the Puritans' efforts to fight the king would have little standing before God, who would consider them just as guilty of sin as Charles. As justice of the peace and a lawyer in the court of wards and liveries, he had played a small role in the corruption of the government. The dire situation demanded radical action–a second Protestant Reformation of sorts like the one a century before when Henry VIII had ended England's affiliation with the Catholic Church. The growing band of separatists–those who disavowed even the Anglican Church–began looking for alternatives. Some fled to Holland and the small New England colony of Pilgrims at Plymouth, Massachusetts. Winthrop himself began to wrestle with how he could live "in this world" if "this world" was evil and impure.

His eventual decision to leave England for North America came after hearing about fellow Puritans' plans to found a new colony in New England where the Puritans could practice their religion purely and wait for the day when England needed their help. In 1628, a year before Winthrop had begun thinking about fleeing England, a group of settlers had received a charter from the Council of New England–which controlled all settlements in New England–to found a small colony. The charter allowed them to settle an area extending from three miles south of the Charles River (where present day Boston is located) to three miles north of the Merrimack River. And, in the closing moments of Charles's final Parliament, the group received a royal charter and changed its name to the Massachusetts Bay Company. Winthrop's son, John, Jr., first presented the idea of joining the new settlers to his father. In the spring of 1629, Winthrop began drafting a statement explaining his decision to leave England. In June, during a brief break between court sessions, Winthrop and his wife decided to make the move.

Winthrop wrestled with the decisions but each time decided that fleeing was the only available answer. Charles's men were arresting Puritans in increasing numbers. The societal corruption might contaminate the younger generations, ending any hope of salvation. Besides, the Puritans could continue God's work and try to convert the American Indians. His friends in the new venture wooed him by saying that he would be one of the few leaders in the New World and would get to help shape the new colony. One final trick by the company's founders helped assure its success. Because of the confusion surrounding the end of Parliament, they had been able to sneak the colony's charter past the king without the common clause saying the new company would be headquartered in London–allowing them to conduct their business in the New World and giving them wider autonomy from the crown. On August 26, Winthrop signed a contract with eleven other Puritan leaders that stated they would be ready to leave for New England the following spring. And on October 20, the Massachusetts Bay Company unanimously selected Winthrop as governor of the new colony from a slate of four candidates.

From this point, everything began happening quickly. When Margaret Tyndal, Winthrop's wife, became pregnant, the family decided that it would be best for her to remain behind in England for at least a little while. Winthrop frantically organized the expedition, gathering everything from ships to horses to provisions to colonists. He tried to restrict the passengers to only the most god-fearing, but he quickly realized the colony would need a wide range of skilled workers. The trip was incredibly expensive for the average family. Some paid in advance, others–mostly tradesmen–were to get land in the new land, and some traveled as indentured servants who would work off their fare at a rate of three shillings a day. Finally, Winthrop needed to arrange some sort of industry for the new colony so it could reward its shareholders back in England. He was able to delay that decision by promising that profits would be distributed at the end of seven years, although it became clear long before then the new colony would never be profitable.

As winter ended Winthrop and a thousand fellow travelers gathered in Southampton to travel to the New World.

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