By this time Rupert had had conferred upon him the title of President of Wales. In February he was at Chester, where applications for help reached him from every quarter. One of the most importunate appeals came from Newark, and thither he decided to go, having appointed the cultured, but ineffective, Sir John Mennes governor of the three northern Welsh counties in his absence. The Royalist cause in North Wales was now beginning to be badly shaken. In September the Roundheads won a great victory at Montgomery, as a result of which the castle fell into their hands. Archbishop Williams, tired and hopeless, was endeavouring to make Conway a refuge for fugitives fleeing from the advancing foe. After the defeat of Marston Moor the disorderly remnants of the King's broken army flocked into Wales, pillaging and rioting, and completing the work of alienating the native inhabitants.

In 1645, however, there was a distinct improvement in the King's fortunes in Wales. Gerard captured Haverfordwest, Picton, and Carew in May, and routed the Parliamentarians of Pembrokeshire. But in June came the King's crushing defeat at Naseby, where the greater part of the Royalist infantry had been Welsh. From the scene of his defeat Charles once more came to Wales to look for another army. But the last great pitched battle had been fought; henceforward the war was made up of sieges and skirmishes. Gerard was still successful; and in quick succession defeated Sir John Price at Llanidloes, Middleton near Oswestry, and Laugharne at Newcastle Emlyn. As a result of these victories the castles of Llanidloes and Cardigan again became Royalist. This time, however, Charles found the Welsh people less eager to listen to his appeals, so bitter was their resentment at the treatment which they had experienced at the hands of the dissolute troopers of Rupert and Gerard. Nevertheless from the Monmouthshire and from the Glamorganshire squires came renewed promises of aid. But even the influence of their landlords failed now to induce the common people to enlist in the King's army. Moreover such recruits as were forthcoming at all were only to be secured by agreeing to certain conditions. They were to have their own Welsh officers; there must be no demand for payment of arrears; and the obligation to entertain soldiers at free quarters must be limited to a single night. Evidently the ancient spirit of sturdy independence was beginning to be roused from its long sleep! Charles had been waiting impatiently at Raglan; then, bitterly disappointed, he proceeded to Chester, and from its walls witnessed the rout of his cavalry at Rowton Heath. At the beginning of 1646 Chester surrendered to Parliament, and in the whole of Wales Harlech Castle alone remained faithful to Charles.

In April 1646 Charles surrendered himself to the Scottish army, and the First Civil War came to an end. Harlech was still holding out, and it was only in March 1647, just a year after the surrender of Chester, and seven months after Raglan, the last English fortress to fly the Royal standard, had capitulated, that it opened its gates to Mytton. The year 1647 was occupied in fruitless negotiations between King and Parliament, and in bitter controversy and recrimination between Parliament and Army, Presbyterians and Independents. So divided had the Roundheads become that Charles again took heart, and in 1648 embarked upon the adventure which was to cost him his life—the so-called Second Civil War. Nowhere had the new religious and political controversies raged with greater rancour than in Wales. The supremacy of the Army, and the triumph of the Independents, were contemplated with unconcealed aversion and dismay. Even men like Laugharne, who had been prominent in the war against Charles, now went over to his side. On February 20, Colonel Poyer, Governor of Pembroke Castle, refused to lay down his command in favour of a successor who had been appointed to take his place. Other bodies of troops joined Poyer, who drove the Parliamentary army out of Pembroke. This was the signal for a general revolt throughout Wales. One-half of the Model Army, under the command of Horton, was sent in hot haste to the Principality; and in May it defeated Laugharne and his rebels at St. Fagan's. Before the end of the month Cromwell himself appeared on the scene. The rebels were chased from the open country, and shut up in the castles of Pembroke, Tenby, and Chepstow. The two latter places were taken without much difficulty, but Pembroke, where Poyer himself commanded, held out until July. Its gallant commander was put to death, to expiate the offence of apostasy, an offence rendered exceptionally heinous by the fact that—to quote the words written by Cromwell at the time—it had been committed "against so much light."

Meanwhile events had been moving quickly in North Wales as well. Byron, with the assistance of Colonel Robinson, had gained possession of Anglesey; but the central figure of the rising in North Wales was the celebrated Sir John Owen of Clenenau. He was a turbulent man, who had done to death the sheriff of Merionethshire with singular brutality. But his undoubted bravery, his bluff manners, and his loyalty made him a popular and a typical figure. Mytton, the successful captor of Harlech, was sent against him, and at the battle of Llandegai Owen was decisively vanquished. With his defeat, and the capture of Pembroke, the Second Civil War in Wales came to a close. Owen had been made prisoner, but through the intercession of Ireton his life was spared.

From the barren, if picturesque, annals of bloodshed, a war in which, so far as Wales was concerned, no great principle was at stake, it is a relief to turn to the settlement of the country under the Commonwealth and Protectorate, and to the work of the few great Welsh Parliamentarians. Colonel John Jones the "Regicide" is deserving at least of passing mention. Brought up in one of the wildest and most remote corners of the Merionethshire mountains, he advanced, by sheer force of character and intellect, to a position of trust in the counsels of Parliament. As soon as war broke out he joined the ranks of the Parliamentary army. We find him representing Merionethshire in the House of Commons in 1647, and again from 1647 to 1653, when he was elected for Denbighshire. No man threw himself with greater zeal into the task of organizing the new army. He was not one of those who, having taken the initial step, cast reluctant glances back. For him there was but one goal—the complete and final victory of Parliament. When this object was attained, he did not hesitate to sit in the Court which sat in judgment upon Charles, nor did he shrink from signing his death warrant. His friendship with Cromwell was cemented by his marriage to the Protector's sister. In Wales, during the war, and in Ireland after its termination, he was an acute and able agent of Parliament, and on one occasion the House of Commons passed a special resolution, thanking him, and voting him a present of £2000. When the Restoration came, John Jones made no effort to escape from the almost certain doom which awaited him by a timely flight abroad; on the contrary he remained openly in London. He was consigned to the Tower, tried, condemned, and put to death with all the horrible barbarities prescribed by the law in the case of traitors.

The other great Welshman of the day was Morgan Llwyd, and with him the whole history of the Commonwealth in Wales is bound up. The victorious Parliament and army, as one might suppose, regarded Wales with no friendly eye; and during the ensuing years the Principality was governed sternly and unsympathetically. The position of Wales varied with the many constitutional experiments of the period. The Agreement of the People, of 1649, proposed to give the country thirty-five representatives out of a total of four hundred. In the Assembly of 1653 Wales had six representatives. Under the Instrument of Government, of 1653, thirty-eight Members, out of four hundred, were allotted to it. But in the hour of its triumph Parliament really counted for little in the affairs of the nation, and the representatives of Wales, mostly strangers, hardly counted at all. It was the great day of officialdom, and the land groaned under their heavy hand.

The new Government, and even the great Protector himself, despite his Welsh descent, cared nothing for Wales as a separate nation; and the national spirit would have fared badly but for a small band of true patriots, the foremost of whom was Morgan Llwyd. This wonderful man was born at Cynfal, a substantial farmhouse situated in one of the most romantic of Merionethshire glens, in the year 1619; and he died in 1659. His life, short as it was, marks the transition from the old Wales to the new, from the condition of poverty, strife, and degrading superstition, to that of freedom, peace, and progress. With the execution of John Roberts of Trawsfynydd, in 1610, perished the last champion of Popery in Wales. With the death of Morgan's own grandfather Huw Llwyd, somewhere about 1630, ended the famous line of poet-magicians who dominated the Welsh mind during the Middle Ages. This Huw Llwyd was, in many respects, a very remarkable man. For many years he had fought on the Continent, in the religious wars of the age; then in his declining years had come to Cynfal, to be the admiration and the terror of his simple neighbours. A belief in witchcraft was then fairly general; and Huw was credited with the possession of unusually extensive authority over the agents of the lower world. In this there was nothing incompatible with a reputation for strict morality, and even sanctity, as one of the very traditions which have been handed down clearly shows. One day Huw was enjoying himself in a tavern in the neighbouring village of Maentwrog. Through the window he descried his friend Archdeacon Edmund Prys go by. Putting his head through the window, he warmly invited him to come in and enjoy the good cheer. The reverend man seems to have been scandalized at the thought; and to show his displeasure he immediately caused two, long horns to grow out of the luckless Huw's head, so that he was unable to withdraw it from the window. Not to be outdone, Huw, that same evening, ordered certain of the devils over whom he had control, to dip the Archdeacon in the mill stream which ran past his house. Such were the merry pranks which parsons and poets played upon each other in early seventeenth-century Wales!

From this atmosphere of superstition Morgan escaped early, being sent to school with Walter Cradock at Wrexham, then the most enlightened centre in the whole country. From his able teacher he learned all the new ideas of freedom both in religion and in politics; and it is not surprising that, when the Civil War broke out, he should have joined the Parliamentary army, and served as chaplain for several years. While in London he united himself with that wonderful sect called the Fifth Monarchy Men. These men believed that the world was destined to be governed by five great monarchies in succession. Four—Assyria, Persia, Greece, and Rome—had already been, and were humbled in the dust. The fifth was to be a heavenly kingdom. Christ would himself appear on earth, would free His saints from bondage, and would establish a universal and immutable empire. They believed His advent to be now at hand, and waited for it anxiously day by day. Their duty, as they conceived of it, was to prepare the way for His coming; and it necessarily followed that an acknowledgment of any earthly monarch must be profane and blasphemous. Fanatical they were, unreasonable they may also have been; but there were no more unflinching upholders of the liberty of the subject, and no better friends of religious toleration. The most influential man in the sect was Harrison, and with his appointment, in 1649, as Governor of South Wales, Morgan Llwyd settled down as pastor at Wrexham.

In February 1650 an Act was passed "for the propagation of the Gospel in Wales." Power was given to commissioners to hold an enquiry into the lives of all the Welsh clergy, and to deprive all such as were found to be immoral, incapable, or hostile to the new Government. A large number actually were ejected, and their place taken by a new and specially certified body of preachers. These commissioners were extremely unpopular in Wales, for the country was strongly anti-Puritan; and much of the unpopularity was visited on the new preachers, who were frequently waylaid and beaten. Not much progress appears to have been made; for as late as 1656 we find Berry, who was Major-General, first for North Wales, and afterwards for South, writing to Thurloe—"One great evil I find here, which I know not how to remedy, and that is the want of able preachers. Certainly, if some course be not taken these people will some of them become heathens."

The "Propagation Act" was repealed in 1653; and that brought to a head the antagonism which for some time had existed between Cromwell and the Fifth Monarchists. The Long Parliament was expelled by Cromwell in 1653; and its successor—the Short Parliament—displayed so marked a leaning in the direction of extreme republicanism, that it soon shared the same fate. Harrison, Vavasour Powell, and Morgan Llwyd were now in open opposition to the Protector; and the two Welshmen toured the Principality inciting the people to rise against him. They stood for complete separation of Church and State, for religious toleration, and for a form of pure democracy in which there would be no room for such an office as that of Protector. Their protest against the Protectorate was published in 1655, under the title of "A Word for God." Morgan Llwyd and Powell were the only two leading Welsh preachers to sign it. That the majority of Welsh Roundheads were entirely favourable to Cromwell is proved by the counter protest which was at once issued, a document which was signed by almost all the leading men, including Walter Cradock. We must allow that Harrison and his followers were unfair to Cromwell in impugning his honesty. The great Protector was always sincere; but he had learnt, what successive generations of politicians have all in turn had to learn, that the ideals of Opposition cannot always be made to square with the facts of Office. The Commonwealth was shipwrecked on the rock of national opposition; the vast majority of the nation were, and continued to be, Royalists and Episcopalians.