While the first batch of 400 new settlers must have been relieved to finally be in New England and at the sight of their new home, the settlement that greeted them could hardly have been comforting. Another 600 settlers would arrive in the next three weeks. They had much work to do before the area would be hospitable. Only about 300 settlers lived in the area, on a few hundred cleared acres around Salem. They lived in shacks and wigwams, based on the Indian design. Beyond the clearings lay uncharted forest, home only to Indians and wild animals. The last winter had claimed eighty of the settlers, and they had few encouraging words for the new settlers. The French and Spanish colonies nearby would occasionally attack the English settlements, and Indians were a constant menace. All in all, the situation looked grim for Winthrop's Puritans.

It cost upwards of fifty pounds for a family to be well provisioned for their new life–a monster sum which few could afford. Many foodstuffs had been lost on the Atlantic crossing, along with livestock and gear. Many only had enough provisions for the summer and fall and would need to find new sources of food to get through the next winter. Dried and salted meat was a staple for the new immigrants, but they needed to find sources of fruit and fresh food to ward off scurvy. Hunting remained a primitive sport, and few settlers had been trained in the use of muskets.

Winthrop quickly set about organizing the settlers and preparing for the next winter–still more than five months away. He tried to set a good example for the rest of the group by working hard and never being idle, and indeed the settlement grew by leaps and bounds in the first months. One beacon for the new settlers was the house of Samuel Maverick, who had constructed a fine house outside Salem and lived in relative comfort. Winthrop believed that if one man could do it, there was no reason the rest of the Puritans could not.

His first task as governor was to locate the best place to start his colony. Finally, after many trips around the area, he settled on the bay around Charlestown, where a small settlement had been started by the Salem colony. The long peninsulas would provide ample room to start the settlement, while making it possible to protect the settlers from attack by Indians or French warships. The settlers busied themselves erecting shelters, some actually digging caves into hillsides and roofing over cellars–hoping the ground would provide good insulation for the coming winter. While the Puritans moved in, Winthrop sent the Lyon back to England to buy more food for the next winter. He sent other men out in small boats to gather or trade for what food they could muster.

He wrote only occasionally to his wife, often saying he had been so busy that he forget to think of her at their appointed time on Mondays and Fridays. He dashed off a quick letter to his son, asking him to bring forty hogshead of meal and assorted other foodstuffs when the boy came over. However, he never expressed any hesitation that the rest of the family should join him in Massachusetts.

One of the biggest problems the settlers faced in their first months was finding a good source of drinking water. The English had been raised to only trust spring water, and Charlestown's single spring could not provide for the entire colony. And after Isaac Johnson and his wife, Lady Arbella, died of diseases possibly related to the water, Winthrop began to look for alternative arrangements. He found an even better location across the harbor on the Boston peninsula. William Blackstone had emigrated from England several years prior and had lived quietly ever since on an estate like Maverick's. Winthrop and most of Charlestown moved across to the new peninsula in early October, even bringing with them the frame house Winthrop had begun constructing. Boston quickly became the political and economical capital of the colony.

Starvation became an increasingly important concern for the colonists as the winter began. By the end of November, Winthrop alone had buried seven of his servants. While Winthrop remained resolute, others in the party were less so. Winter began in earnest the day before Christmas, when a giant storm struck the colony. Frostbite exacted a heavy price from the colonists, and several huts were lost that winter after the fires inside grew too large and caught the thatched roofs on fire. In Winthrop's journal, he relates the story of six colonists marooned on Cape Cod in December. Only two survived. The entire colony might have been lost that first winter except that the Lyon arrived in February bearing with it a hold full of food–most importantly, it brought lemon juice to ward off scurvy. When the ship prepared to leave again, it carried with it eighty passengers who hoped to leave New England behind forever.

More than 200 settlers died in the first winter and an equal number had fled the colony when the winter ended. But Winthrop and the other survivors saw that the worst was behind them and that another summer to rebuild would make the future winters bearable. He wrote home triumphantly at the end of the winter, "I want nothing but thee and the rest of my family."

Over the second summer, Winthrop laid out plans for a six hundred acre farm and a large stone house on the Mystic River, and he secured more funding for the colony, mostly by dipping into his own finances. As the colony expanded, it came to need a business to support it. For the first year or so, the colonists found they could make a good business selling lumber and crops to the newly arriving immigrants. Indeed, the immigrants often came laden down with the goods the colonists needed, like pots and pans, tools, and clothing. Winthrop also began building up the colony's shipping industry so it could trade sassafras and hemp with England.

In the fall of 1631, Margaret and rest of Winthrop's family arrived in Massachusetts amid a great celebration by the colonists, who wanted to thank Winthrop for his work saving the colony. It was apparent to the colonists by that time that God had smiled on their new venture and rewarded them for trying to live a pure life. The colony was secure.

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