Getting ballast, overhauling rigging, getting wood, water, etc., from shore.
Christopher Jones had certainly not intended to spend the winter in New England: the Mayflower, of which he was part owner, had left England too late in the year, and then the settlers took too long to find a place to settle, and then they took too long to build a place to live and move their goods to shore, and then most of his crew got sick. Those who did not die were too sick to sail back across the ocean in the winter. If the Pilgrims had arrived when they were originally supposed to, they would have been able to grow at least a little produce to send back, along with any other commodities that they could have sent back for sale in England (such as furs) to pay back the Adventurers. The winter was cold, and no work was possible except for what was needed for immediate, hand-to-mouth necessities. Jones could have waited until the summer, and perhaps have brought back some things, but he clearly was not all that optimistic about what could be produced. The lack of cargo meant that the ship lacked ballast; it was probably loaded with stones from the beach, but stone was not really something of which England was in need. And they had run out of beer, so the crew would have to drink water. All the way back.