The Separatists attempted to obtain exemption through petitions to the Assembly, trusting that, as each new election sent more and more New Lights to that body, each prayer for relief would be more favorably received. One of the most important of these petitions was that of 1753, when more than twenty Separatist churches, representing about a thousand members, united in an appeal wherein they complained of the distraining of their goods to meet assessments and taxes for the benefit of the Established churches; of imprisonments, with consequent deprivation of comforts for their families; and of the danger to the civil peace threatened by these evils. The Assembly refused redress. Whereupon the petition was at once reconstructed,[a] and, with authentic records and testimonies, to which Governor Fitch set the seal of Connecticut, was sent, in 1756, [134] to London. The Committee in behalf of Dissenters were to see that it was presented to the King in Council. The petition charged violation of the colony's charter, excessive favoritism, and legislation in favor of one Christian sect to the exclusion of all others and to the oppression, even, of some. The English Committee thought that these charges might anger the King and endanger the Connecticut charter. Accordingly, they again wrote to the Connecticut authorities, remonstrating with them because of their treatment of dissenters. At the same time, they sent a letter advising the petitioners to show their loyalty to the best interests of the colony by withdrawing their complaint. These dissenters were further advised to begin at once a suit in the Connecticut courts for their rights, and with the intent of carrying their case to England, should the colony fail to do them justice. Legal proceedings were immediately begun, but were allowed to lapse, partly because of the press of secular interests, for the colonial wars, the West India expedition, and other affairs of great moment claimed attention, and partly because there were indications that the government would regard the Separatists more favorably.
In the colony itself a change was taking place through which the college was to go over to the side of the New Lights. In 1755, President Clap had established the College Church in order to remove the students from the party strife that was still distracting the churches. In order to avoid a conflict over the matter, he refused to ask the consent of the Assembly, claiming the right of an incorporated college and the precedent of the English universities, since, in 1745, the Assembly had formally incorporated "The President and Fellows of Yale College," vesting in them all the usual powers appertaining to colleges. In the same year, also, the initial step toward establishing a chair of divinity had been taken, and it became the first toward the founding of the separate College Church. President Clap always maintained that "the great design of founding Yale was to educate ministers in our way,"[135] and the chair of divinity had been established in answer to the suggestion of the Court that the college take measures to protect its students from the New Light movement. President Clap was hurried on in his policy of establishing the College Church both by his desire to separate the students from the New Light controversy in Mr. Noyes's church, where they were wont to attend, and by an appeal to him, in 1753, of Rector Punderson, the priest recently placed in charge of the Church-of-England mission in New Haven. The rector had two sons in college, and he asked that they and such other collegians as were Episcopalians might be permitted to attend the Church-of-England services. President Clap refused to give the desired permission, except for communion and some special services, and he at once proceeded to organize a church within the college. The trustees and faculty upheld him, but the Old Lights, then about two-thirds of the deputies to the Assembly, opposed his course of action, and succeeded in taking away the annual grant that, at the incorporation of the college, had been given to Yale. After this, they regarded President Clap as a "political New Light," but as the latter party increased in the Assembly, and became friendly to Yale, the college gradually reinstated itself in the favor of the legislature.