"With as much zeal, devotion, piety, He always lived as other saints do die. Still with his soul severe account he kept, Weeping all debts out ere he slept; Then down in peace and innocence he lay, Like the sun's laborious light, Which still in water sets at night, Unsullied with the journey of the day."

Cowley's friendship with this family affected the course of his life. He received many kindnesses from his friend's brother John Hervey, including introduction to Henry Jermyn, one of the most trusted friends of Queen Henrietta Maria, the friend who was created by her wish Baron Jermyn of St. Edmondsbury, who was addressed by Charles I. as "Harry," and was created by Charles II., in April, 1660, Earl of St. Albans. He was described in Queen Henrietta's time by a political scandal-monger, as "something too ugly for a lady's favourite, yet that is nothing to some." In 1643 Cowley was driven from Cambridge, and went to St. John's College, Oxford. To Oxford at the end of that year the king summoned a Parliament, which met on the 22nd of January, 1644. This brought to Oxford many peers and Royalists, who deserted the Parliament at Westminster for the king's Parliament at Oxford. It continued to sit until the 16th of April, by which time the king had found even his own Parliament to be in many respects too independent. In 1644 the queen, about to become a mother, withdrew to Exeter from Oxford, against which an army was advancing; and the parting at Oxford proved to be the last between her and her husband. A daughter was born at Exeter on the 16th of June. Within two weeks afterwards the advance of an army towards Exeter caused the queen to rise from her bed in a dangerous state of health, and, leaving her child in good keeping, escape to Plymouth, where she reached Pendennis Castle on the 29th of June. On the 2nd of July the king's forces were defeated at Marston Moor. On the 14th of July the queen escaped from Falmouth to Brest. After some rest at the baths of Bourbon, she went on to Paris, where she was lodged in the Louvre, and well cared for. Jermyn was still her treasurer, her minister, and the friend for whose counsel she cared most.

It was into the service of this Lord Jermyn that Cowley had been introduced through his friendship with the Herveys. He went to Paris as Lord Jermyn's secretary, had charge of the queen's political correspondence, ciphered and deciphered letters between Queen Henrietta and King Charles, and was thus employed so actively under Lord Jermyn that his work filled all his days, and many of his nights. He was sent also on journeys to Jersey, Scotland, Flanders, Holland, or wherever else the king's troubles required his attendance. In 1647 Cowley published his volume of forty-four love poems, called "The Mistress." He was himself no gallant, neither paid court to ladies, nor married. His love poetry was hypothetical; and of his life at this time he says: "Though I was in a crowd of as good company as could be found anywhere; though I was in business of great and honourable trust; though I ate at the best table, and enjoyed the best convenience for present subsistence that ought to be desired by a man of my condition in banishment and public distresses, yet I could not abstain from renewing my old schoolboy's wish in a copy of verses to the same effect:-

"'Well, then, I now do plainly see This busy world and I shall ne'er agree,' &c.,

and I never then proposed to myself any other advantage from his Majesty's happy restoration, but the getting into some moderately convenient retreat in the country, which I thought, in that case, I might easily have compassed, as well as some others who, with no greater probabilities or pretences, have arrived to extraordinary fortunes."

In 1654 Queen Henrietta, under influence of a new confessor, had left the Louvre, and, with the little daughter born at Exeter, taken up her quarters in a foundation of her own, at Chaillot, for nuns of the visitation of St. Mary. Lord Jermyn having little use left for a secretary in Paris, Cowley in 1656, after twelve years' service in France, was sent to England that he might there live in the retirement he preferred, and with the understanding that he would be able to send information upon the course of home affairs. In England he was presently seized by mistake for another man, and, when his name and position were known, he was imprisoned, until a friendly physician, Sir Charles Scarborough, undertook to be security in a thousand pounds for his good conduct. In this year, 1656, Cowley published the first folio volume of his Poems, prepared in prison, and suggested, he said, by his finding, when he returned to England, a book called "The Iron Age," which had been published as his, and caused him to wonder that any one foolish enough to write such bad verses should yet be so wise as to publish them under another man's name. Cowley thought then that he had taken leave of verse, which needed less troubled times for its reading, and a mind less troubled in the writer. He left out of his book, he said, the pieces written during the Civil War, including three books of the Civil War itself, reaching as far as the first battle of Newbury. These he had burnt, for, he said, "I would have it accounted no less unlawful to rip up old wounds than to give new ones." "When the event of battle and the unaccountable Will of God has determined the controversy, and that we have submitted to the will of the conqueror, we must lay down our pens as well as arms." The first part of this folio contained early poems; the second part "The Mistress;" the third part "Pindaric Odes;" and the fourth and last his "Davideis."

In September of the following year, 1657, Cowley acted as best man to George Villiers, Duke of Buckingham, on his marriage at Bolton Percy, to Fairfax's daughter; Cowley wrote also a sonnet for the bride. In December he obtained, by influence of friends, the degree of M.D. from the University of Oxford, and retired into Kent to study botany. Such study caused him then to write a Latin poem upon Plants, in six books: the first two on Herbs, in elegiac verse; the next two on Flowers, in various measures; and the last two on Trees, in heroic numbers:- "Plantarum, Libri VI."

After the death of Cromwell, Cowley returned to France, but he came back to England in 1660, when he published an "Ode on His Majesty's Restoration and Return," and "A Discourse by way of Vision concerning the Government of Oliver Cromwell." He was admitted, as Dr. Cowley, among the first members of the Royal Society then founded; but he was excluded from the favour of the king. He had written an "Ode to Brutus," for which, said his Majesty, it was enough for Mr. Cowley to be forgiven. A noble lord replied to Cowley's Ode, in praise of Brutus, with an Ode against that Rebel. Cowley's old friend, Lord Jermyn, now made Earl of St. Alban's, joined, however, with George Villiers, Duke of Buckingham, in providing for the poet all that was required to secure to him the quiet life that he desired. Provision to such end had been promised him both by Charles I. and Charles II., in the definite form of the office of Master of the Savoy, but the post was given by Charles II. to a brother of one of his mistresses.