One of the first steps taken by the company under the new charter was to organize a temporary local government for the colonists in Massachusetts.  This was to consist of a governor, a deputy governor, and thirteen councillors, of whom seven were to be named by the company, three were to be chosen by these seven and the governor, and three more were to be appointed by the “old planters” found in Massachusetts at the arrival of Endicott.  Land was allotted on a plan like that adopted by the London Company:  each shareholder was to have two hundred acres for every L50 that he invested, and if he settled in that country, fifty more for himself and fifty more for each member of his family.[11]

A letter of instructions was draughted, April 17, to Governor Endicott, in which mention was made of the negotiations with Oldham, and orders given to effect an occupation of the territory covered by his grant from John Gorges.  This letter was sent off by a special ship which reached Salem June 20, 1629, and Endicott promptly despatched three brothers of the name of Sprague, and a few others, who planted themselves at Mishawum, within the disputed territory, where they found but “one English palisadoed and thatched house wherein lived Thomas Walford, a smith.”  Other emigrants followed, and there, in July, was laid out by Endicott a town which was named Charlestown.  This practically ended the difficulty with Oldham, who was kept in the dark till the ship sailed from England, and was then told by the company that they were determined, on advice of counsel, to treat his grant as void.  As for Brereton, he was made a member of the company and did not give any real trouble.[12]

May 11, 1629, sailed from London five ships carrying about four hundred settlers, most of whom were servants, and one hundred and forty head of cattle and forty goats.  They arrived at Salem, June 27, and about four weeks later the ecclesiastical organization of the colony was effected by John Endicott, who had already written to Bradford that the worship at Plymouth was “no other than is warranted by the evidence of the truth.”  He set apart July 20 for the work, and, after a portion of the morning spent in prayer, Samuel Skelton and Francis Higginson, two of the four ministers who accompanied the last arrivals, avowed their belief in the doctrines of the Independents, and were elected respectively pastor and teacher.  A confession of faith and a church covenant were drawn up, and August 6 thirty persons associated themselves in a church.[13]

Two of the gentlemen emigrants, John and Samuel Browne, presumed to hold a separate service with a small company, using the Prayer Book.  Thereupon the hot-headed Endicott arrested them, put them on shipboard, and sent them back to England.  This conduct of Endicott’s was a flagrant aggression on vested rights, since the Brownes appear in the charter as original promoters of the colony, and were sent to Massachusetts by the company in the high capacity of assistants or councillors to Endicott himself.  The two brothers complained in England, and in October, 1629, the company sent Endicott a warning against “undigested counsels ... which may have any ill construction with the state here and make us obnoxious to an adversary."[14]