Besides his academic and literary concerns, Owen was continually involved in affairs of state. In 1651, on 24 October (after Worcester), he preached the thanksgiving sermon before parliament. In 1652 he sat on a council to consider the condition of
Protestantism in
Ireland. In October 1653 he was one of several ministers whom Cromwell summoned to a consultation as to church union. In December, the degree of
Doctor of Divinity was conferred upon him by Oxford University. In the
First Protectorate Parliament of 1654 he sat, for a short time, as the sole member of parliament for
Oxford University, and, with Baxter, was placed on the committee for settling the "fundamentals" necessary for the toleration promised in the Instrument of Government. In the same year he was chairman of a committee on Scottish Church affairs. He was, too, one of the Triers, and appears to have behaved with kindness and moderation in that capacity. As vice-chancellor he acted with readiness and spirit when a Royalist rising in
Wiltshire broke out in 1655; his adherence to
Cromwell, however, was by no means slavish, for he drew up, at the request of Desborough and Pride, a petition against his receiving the kingship. Thus, when
Richard Cromwell succeeded his father as chancellor, Owen lost his vice-chancellorship. In 1658 he took a leading part in the conference of Independents which drew up the
Savoy Declaration (the doctrinal standard of
Congregationalism which was based upon the
Westminster Confession of Faith). On Oliver Cromwell's death in 1658, Owen joined the
Wallingford House party, and though he denied any share in the deposition of
Richard Cromwell, he preferred the idea of a simple republic to that of a protectorate. He assisted in the restoration of the
Rump Parliament, and, when
George Monck began his march into England, Owen, in the name of the Independent churches, to which Monck was supposed to belong, and who were anxious about his intentions, wrote to dissuade him. In March 1660, the
Presbyterian party being uppermost, Owen was deprived of his deanery, which was given back to Reynolds. He retired to Stadham, where he wrote various controversial and theological works, in particular his laborious
Theologoumena Pantodapa, a history of the rise and progress of theology. The respect in which many of the authorities held his intellectual eminence won him an immunity denied to other Nonconformists. In 1661 the celebrated
Fiat Lux, a work by the
Franciscan friar John Vincent Cane, was published; in it, the oneness and beauty of
Roman Catholicism are contrasted with the confusion and multiplicity of Protestant sects. At
Clarendon's request Owen answered this in 1662 in his
Animadversions; and so great was the success of that work that he was offered preferment if he would conform. Owen's condition was liberty to all who disagreed in doctrine with the
Church of England; nothing therefore came of the negotiation. In 1663, Owen was invited by the Congregational churches in
Boston, Massachusetts, to become their minister, but declined. The
Conventicle and
Five Mile Acts drove him to London; and in 1666, after the
Great Fire, he, like other leading Nonconformist ministers, set up a room for public service and gathered a congregation, composed chiefly of the old Commonwealth officers. An 1862 source says "this congregation was distinguished more for the rank and worth of its members than for its numbers" and gives as examples
John Desborough, the soldier who married Cromwell's sister;
James Berry (Major-General), another soldier;
Charles Fleetwood, the soldier who married Cromwell's daughter;
Bridget Bendish, Fleetwood's stepdaughter;
Sir John Hartopp and his wife, Fleetwood's daughter Elizabeth;
Mary, Lady Abney of
Abney Park, next door neighbour to the Fleetwoods; and
Lady Haversham. Meanwhile, Owen was incessantly writing; and in 1667 he published his
Catechism, which led to a proposal, "more acute than diplomatic", from Baxter for union. Various papers passed, and after a year the attempt was closed by the following laconical note from Owen: "I am still a well-wisher to these mathematics." It was now, too, that he published the first part of his vast work upon the
Epistle to the Hebrews, together with his
Practical Exposition upon Psalm 130 (1668) and his searching book on
Indwelling Sin, which
Alexander Whyte described as "one of the greatest works of the Puritan period." In 1669, Owen wrote a spirited remonstrance to the Congregationalists in
New England, who, under the influence of Presbyterianism, had shown themselves persecutors. At home, too, he was busy in the same cause. In 1669
Samuel Parker's
Discourse of Ecclesiastical Politie attacked the Nonconformists with clumsy intolerance. Owen answered him (
Truth and Innocence Vindicated, 1669); Parker replied offensively in his
Defence and Continuation of the Ecclesiastical Politie (1671). Then
Andrew Marvell finally disposed of Parker with banter and satire in ''The Rehearsal Transpros'd
(1672 and 1673). Owen himself produced a tract On the Trinity
(1669), and Christian Love and Peace'' (1672). On the revival of the Conventicle Acts in 1670, Owen was appointed to draw up a paper of reasons which was submitted to the
House of Lords in protest. In this or the following year
Harvard College invited him to become its president; he received similar invitations from some of the Dutch universities. When King
Charles II issued his
Declaration of Indulgence in 1672, Owen drew up an address of thanks; Owen was one of the first preachers at the weekly lectures which the Independents and Presbyterians jointly held at Princes' Hall in Broad Street. He was respected by many of the nobility, and during 1674 both
King Charles II and his brother
King James II assured him of their good wishes to the dissenters. Charles gave him 1000 guineas to relieve those on whom the severe laws had pressed, and he was able to procure the release of
John Bunyan, whose preaching he admired. In 1674 Owen was attacked by
William Sherlock, Dean of
St Paul's. From this time until 1680, he was engaged on his ministry and writing. He had
Alexander Shields as his
amanuensis for a while. ==Later life==