That fall Theophilus Eaton led an exploration party south to the north shore of Long Island Sound in search of a suitable site. He purchased land from the Indians at the mouth of the Quinnipiac River. In the spring of 1638 the group set out, and on April 14 they arrived at their 'New Haven' on the Connecticut shore. The site seemed ideal for trade with a good port between Boston and New Amsterdam and access to the furs of the Connecticut River valley. However, while the colony succeeded as a settlement and religious experiment, its future as a trade center was some years away.
In 1639 they adopted a set of Fundamental Articles for self-government, partly as a result of a similar action in the river towns. A governing council of seven was established, with Eaton as chief magistrate and Cunningham as pastor. The articles required that "...the word of God shall be the only rule..." and this was maintained even over English common law tradition. Since the Bible contained no reference to trial by jury, they eliminated it and the council sat in judgment. Only members of their church congregation were eligible to vote.
Later Branford joined in 1643 and was the last the official "plantations" in the New Haven Confederation . They based their government on that of Massachusetts but maintained stricter adherence to the Puritan discipline.
The treaty which placed no westward limit on the land west of the Delaware was to be the legal basis for a Connecticut "sea to sea" claim of owning all the land on both sides of the Delaware from the Atlantic Ocean to the Pacific Ocean.
In 1642 fifty families on a ship captained by George Lamberton settled at the mouth of Schuylkill River around to establish the trading post at what is today Philadelphia. The Dutch and Swedes who were already in the area burned their buildings. A Swedish court was to convict Lamberton of "trespassing, conspiring with the Indians.
The New Haven Colony would not get any support from its New England patrons and Puritan Governor John Winthrop was to testify that the "Delaware Colony" "dissolved" owing to summer "sickness and mortality.
According to legend a year and half later in 1647 following a thunder shower an apparition of the ship appeared on horizon. Those on shore were said to have recognized their friends on deck. The ship's masts then appeared to snap, and in the pitch the passengers were thrown into the sea and the ship capsized. Town fathers were to say the event gave them closure.
Henry Wadsworth Longfellow wrote the poem "The Phantom Ship" about the event which includes the lines:
The disasters in Philadelphia and sinking of its ship were to weaken the Colony's future negotiating position.
In 1661, the judges who had signed the death warrant of Charles I of England in 1649 were pursued by Charles II. Two judges, Colonel Edward Whalley and Colonel William Goffe, fled to New Haven to seek refuge from the king's forces. John Davenport arranged for these "Regicides" to hide in the West Rock hills northwest of the town. A third judge, John Dixwell, joined the other regicides at a later time.
Many factors were to contribute to the loss of power including the loss of its strongest governor Eaton, the economic disasters of losing its only ocean going ship and the Philadelphia disaster. Also there was the regicide case. The New Haven Colony harbored several of the regicide judges who sentenced King Charles I to death. The New Haven Colony was absorbed by the Connecticut Colony partly as royal punishment by King Charles II for harboring the regicide judges who sentenced King Charles I. At the same time the Connecticut Colony had seen its star rise.