According to Ivan Roots, the eventual ecclesiastical settlement under the Protectorate followed closely proposals from 1652, outlined by Nye with John Owen and others.
Nye along with Stephen Marshall "were sent with the commissioners who went from the English Parliament into Scotland, in order to obtain and establish an agreement with the Scottish nation, and to desire their assistance.
[17] Nye and Goodwin co-authored An Apologeticall Narration, pleading for toleration of Calvinist congregations outside a proposed Presbyterian national church.
[18] Their text presented to Parliament on 3 January 1644 argued that Congregational churches were closer to the practice of early Christians and more suited to the changeability of the times.
[19] In the Whitehall Debates of 1648, however, Nye backed Henry Ireton's view that toleration should be limited by the state and joined in opposing the Racovian Catechism.
Their plea had Cromwell's direct encouragement, although wild anti-Semitic rumours and general public antipathy made readmission politically impossible.