June 1631 found Hooker in the Netherlands, his wife and children meanwhile being cared for, it seems, on the Earl of Warwick's estate at Great Waltham. Two things marked Hooker's stay in the Netherlands, first his harmonious assistantship to the exiled Scots minister, John Forbes, who ministered to English-speaking merchants in the Prinsenhof Church at Delft, and, second, his meeting and friendship with the great William Ames, whom he had last seen in Cambridge in 1610. If Ames remembered the young Fellow of Emmanuel he certainly found him now to be a different man. Cotton Mather records Ames' assertion that 'though he had been acquainted with many scholars of divers nations, yet he never met with Mr Hooker's equal, either for preaching or for disputing'. These were memorable words in a generation of men who were not given to praising one another.
In March, 1633, or thereabouts, Hooker left Delft for Rotterdam and appears to have made a short visit to England to ascertain both for himself and Forbes the prospect in New England. It may well have been shortly before that visit that he wrote to John Cotton (in hiding in England), advising him that he saw no cause to encourage fellow countrymen to settle in the Netherlands and going on to speak of his own perplexity in knowing the guidance of God:
My ague yet holds me. The ways of God's providence, wherein he has walked towards me in this long time of my sickness and wherein I have drawn forth many wearyish hours under his Almighty hand (Blessed be his Name!), together with pursuits and banishment which have waited upon me, as one wave follows another, have driven me to an amazement, his paths being too secret and past finding out by such an ignorant, worthless worm as myself. I have looked over my heart, and life, according to my measure, aimed and guessed as well as I could, and entreated his Majesty to make known his mind, wherein I missed. And yet methinks I cannot spell out readily the purpose of his proceedings, which, I confess, have been wonderful in miseries and more than wonderful in mercies to me and mine.
Probably Hooker's visit to England decided his mind as he met and conferred with old friends. The emigration to New England of which he had spoken publicly in 1631 was quickening in pace. A number of his Essex hearers and converts were already at Mount Wollaston in Massachusetts Bay by August 1632, being known as 'Mr Hooker's company'. Others were ready to leave. These former hearers pressed him to join them, and to bring Samuel Stone with him as an assistant. When 'aged and holy Mr Forbes', as Mather calls him, heard the hopeful news when Hooker returned to the Netherlands he nevertheless decided to stay in the land where he was to die in 1634. In the early summer of 1633 Hooker was back in England, experiencing escapes from arrest which were not due to any lack of effort on the part of the authorities. At length with his wife and their children, with John Cotton, Samuel Stone, and some 200 others they sailed from the Downs on the Griffin in July, 1633. 'None but Mr Stone was owned for a preacher at their first coming abroad,' writes Mather, 'the other two delaying to take their turns in the publick worship of the ship till they were got so far into the main ocean that they might with safety discover [reveal] who they were.'
Forty-eight years old when he arrived in Boston, Massachusetts, on September 4, 1633, Hooker and Stone first served the church formed at Newtown (Cambridge) and then, in July, 1636, removed to Hartford where, in due course, the new colony of Connecticut was formed beside the river from whence it took its name. Differences in opinion between Hooker and some of the leaders in Boston undoubtedly contributed to the decision to remove further from the Bay. These differences did not concern the doctrine of conversion or the fundamentals of the gospel; on these things Hooker ever remained in union with his brethren; they had to do rather with the political policy in Massachusetts. The counsel which prevailed in Boston, influenced by the assumption that at various points a Christian state should follow the Old Testament theocracy, restricted suffrage to church members and was ready to deal with differences of religious opinion by force of law. Hooker saw the error in this thinking. Along with all Puritans, 'Hooker held that the care of the Church was the first duty of the magistrate, and that civil laws for the support of a chosen Church were salutary for both Church and State. But,' writes Sanford H. Cobb, 'he never attempted to blend the two together'. The existence of greater religious liberty in Connecticut is directly attributable to the man whom Mather calls 'the chief instrument' in its beginning.
His wisdom on the state and church issue was not to be the principal thing for which Hooker was to be remembered after his death in July, 1647. As with Paul, the chief commendation of his ministry, was supplied by the men and women who had become 'the epistle of Christ ministered by us, written not with ink but with the Spirit of the living God'. In the opinion of Winthrop, noted in his journal, at the time of the passing of New England's 'Luther': 'The fruits of his labours in both Englands shall preserve an honourable and happy remembrance of him forever'. This brings us back, then, to the subject of conversion and to the preaching which was the instrument of drawing many to Christ. We have already noted how Samuel Collins, Laud's informer, warned that even with Hooker silenced in Chelmsford 'his genius will still haunt all the pulpits in the country'. What that 'genius' was, in respect to the preaching of the gospel, it remains for us to consider.