A little more History: (I would highly recommend reading all of the works referenced below. You will find them tremendously profitable to both mind and heart.)
In 1653 Owen was once more engaged in preaching before Parliament. In the midst of these engagements, Cromwell invited him, together with a number of other ministers -- Presbyterian, Independent, and Baptist -- to hold a conference on Christian unity. Apparently too much was attempted and no practical measures resulted. But at least it showed the willingness and earnest desire of the leaders to confer together and recognize each other as brethren in the same family.
Baxter, Howe and Owen were all champions of unity and of the advance of Christian love. Baxter wrote: “While we wrangle here in the dark, we are dying, and passing to the world that will decide all our controversies; and the safest passage thither is by a peaceable holiness.” Howe was of kindred spirit, and in this vein wrote his essay On Union among Protestants and On the Carnality of Religious Contentions. Owen shared the same ideals and laboured with tongue and pen to motivate towards a greater expression of unity.
He was wise enough to picture denominational differences in their right proportion, neither disregarding them nor blowing them up. Two of his early works, The Duty of Pastors and People Distinguished and Eshcol: or, Rule for Church Fellowship deal with this important theme.
Owen’s major contribution, together with the efforts of other Puritans, was in expounding in their writings the major principles on which true and lasting unity can be accomplished. In their mind unity, love and sound doctrine do not repel each other; they are complementary and must be found together at all times.
Owen fought on two fronts: on one hand he had to maintain a ministry of warning to his brethren against the inroads of Popery, and on the other hand heroically holding to the ideal of unity among brethren. He longed to see the ranks of the true church of Christ marching on to victory, with all alienations and divisions healed or at least placed in their proper perspective and reduced to their true magnitude. He wanted the Protestant denominations to cultivate a spirit of mutual confiding so as to be prepared in their resistance to their common enemy.
Nevertheless he was still convinced of the necessity and duty of separation from the Episcopal Church. Engaged in controversy with Stillingfleet he produced one of his best apologies of Nonconformity, entitled, A Brief Vindication of Nonconformists from the Charge of Schism, as it was managed against them in a Sermon by Dr Stillingfleet. Still, he was convinced that evangelicals, whose faith is embedded in Scripture alone, have a solemn duty to “keep the unity of the Spirit in the bond of peace.” In this respect he produced such studies as Union among Protestant, a work expressing this generous intent and desire.