At the same time, active measures were taken to secure both the devotion and efficiency of the fleet. According to the uniform practice of the Long Parliament, the administration was kept in the hand of an Admiralty Committee of members of Parliament. Under them there was a Navy Committee, consisting of officials who discharged the duties of the Treasurer, Surveyor, Comptroller, and Clerk. Both bodies were composed of able and zealous men, by whom the work of administration was excellently done. During the first years of the Commonwealth, the navy made great strides both in number and quality. Ships were so rapidly built that the effective strength was as good as doubled between 1649 and 1651. The work of building was largely done by the Petts, who were now so effectually established in the dockyards that it would have been impossible to replace them by an equally competent body of officials. Nor, although their grasping spirit made them unpopular, was there any reason for getting rid of them. The Pett family served its successive masters with the undeviating loyalty of the Vicar of Bray. For them the commanding interest of the nation was that they should retain their places. During these earlier years the Commonwealth was also comparatively rich. It had not yet to bear the strain of the great Dutch war, and it had not exhausted the resources afforded by the confiscated estates of the Church, the Crown, and the Royalists, nor had it yet used up the fines levied on the king's party for the sin of Delinquency. Therefore it was able not only to build ships rapidly and well, but also to pay the sailor with a regularity to which he had not hitherto been accustomed. The wealth of the Government, and the need it had for his services, were, for a time, of immense benefit to the sailor. His pay had been raised from 15s. to 19s. a month during the Civil War. Under the Commonwealth it was increased to 23s. for able seamen, and 19s. for ordinary seamen. As much as 25s. a month were given to the men engaged on particular service, such as the pursuit of Rupert. Measures were also taken to give the men a fairer share of prize-money, and to secure its rapid and honest distribution. Government had hitherto looked upon prizes taken from the enemy as a resource. Being in chronic want of money, it had treated its men with scant generosity. The evidence both of Sir William Monson and Sir Richard Hawkins shows that Elizabeth's sailors expected little justice at the hands of her officers. The Commonwealth was soon beset by the same necessities as the Crown, and yielded to the temptation of throwing as many charges as possible on the Commissioners for prizes. Yet it did try to be handsome in its behaviour towards its servants, who for a time, before and after the establishment of Cromwell as Protector, profited both in pay and prize-money to a hitherto unknown extent. At no time do they seem to have been so badly used as they had been under Charles I., and were again to be under Charles II. Pay and prize-money were not all. Care was taken to supply better food, and more of it. The observance of Lent, which had hitherto enabled the State to economise meat rations, was abolished; though this was probably mainly done by the Puritans from a religious motive. Better pay, more prize-money, and good feeding had the desired effect of securing the loyalty of the seamen. We may at any rate attribute to them at least as much effect in keeping the sailors steady to the Commonwealth as to their high conception of that duty of preventing foreigners from "fooling us," which is sometimes supposed to have supplied their main motive.

The work before the navy of the Commonwealth at the beginning of 1649 was sufficiently abundant and varied. The Royalists still held the Channel Islands, and Ireland was unsubdued. Besides this, the English settlements in America had not yet been brought to submission to the new Government. The Puritan colonies were indeed thoroughly in sympathy with the Commonwealth, but Virginia was Royalist, and Barbadoes, then our only footing in the West Indies, was held for the king. An even more pressing duty than the subjugation of Royalist strongholds in the Channel and the West Indies lay before the Commissioners who had succeeded Warwick in the command of the fleet.

When the Parliament's fleet retired from Helvoetsluys, carrying with it the revolted ships which had returned to their duty, it left a remnant of seven vessels in the service of the Prince of Wales. It was natural that he should endeavour to make use of these vessels for the cause. The manner of using them was imposed upon him by circumstances. They could not hope to meet the Commonwealth's naval forces in open conflict, but they could prey upon the commerce of the king's disloyal subjects. It might have been wiser not to yield to the temptation of using them in a species of warfare which could hardly help becoming piratical, but the need for money was great, the technical right of the king to fight for his crown on the sea was at least as good as his right to continue the struggle by land, and the prince did what it would have required exceptional wisdom and virtue to restrain him from doing. He appointed Prince Rupert as his admiral, with the proviso that he was to vacate the place to the Duke of York if called upon, and issued commissions authorising him and his captains to make prize of all the king's English enemies, and all such foreigners as should give them help. It was one thing to appoint an admiral and give him a commission, and quite another to fit the ships for sea. The exiled king had no money. He expected his squadron to provide him with funds. The ships must be got to sea somehow. A resource was found by selling the guns of the Antelope, and with the money thus provided another of the ships at Helvoetsluys was armed for sea. A lucky privateering cruise brought in funds, and with them the remainder were armed.

Rupert left Helvoetsluys in January 1649, with a squadron of seven warships and one armed prize. This was the whole naval force which now supported the Royal Standard of England. It ran down Channel and made for Kinsale. The blockade of this port had been raised by Parliament on the recommendation of Colonel Edward Popham. Prince Rupert entered it with the ships which had accompanied him from Helvoetsluys, and perhaps with some prizes he had picked up on the way. From this harbour he began cruising against English commerce with such success, that whereas the remnant of His Majesty's navy had lately been in extreme distress, it was now able to boast itself rich. A further service was rendered to the Royalist cause by the relief of the garrison still holding the Scilly Isles for the king. Prince Rupert was struck by the advantages this group of islands seemed capable of affording to an enterprising leader engaged in harrying commerce. He thought they might be turned into another Venice. Another Algiers would have been a more accurate expression. His schemes for making the Scilly Isles a basis of operations against the commerce of England were nipped in the bud by the naval forces of the Parliament. One of his ships was captured after a hot fight by two of the Commonwealth cruisers, and this misfortune seems to have been received as a sharp warning by its comrades. They returned to Kinsale, and, while engaged in getting ready for a summer cruise, were disagreeably surprised by the appearance of a strong blockading force under the command of Sir George Ayscue. Ayscue was soon called away to other service, but his place was taken by two of the new admirals and generals at sea, Blake and Deane. They held Rupert so closely blockaded until October, that not only were his raids against commerce entirely stopped, but great discontent arose among his men, who were reduced to idleness and threatened by want. Many deserted, and Rupert was compelled to disarm some of the prizes which he had been fitting for sea. After the first successes of Cromwell had made it clear that the king's cause was ruined in Ireland, the position of Rupert at Kinsale became one of extreme danger. If the blockade had continued until the Puritan army was upon the town, it is eminently probable that, unless Rupert had been slain in action, he would have followed Hamilton and Culpepper to the block. A heavy gale released him from this peril. It drove the forces of the Parliament off the coast, and gave Rupert an opportunity of escaping of which he did not fail to avail himself. With his original seven ships, but without his prizes, he sailed for Portugal. The overwhelming naval strength of the Parliament in the Channel had rendered his original scheme of holding the Scilly Isles impracticable.

On his way south he fell in with and captured some English merchant ships near the Berlings. Rejoiced by this booty, which he calculated would be worth forty thousand pounds to the king's service, he entered the Tagus. At Kinsale he had heard of the execution of King Charles, and had received a confirmation of his commission from the new king. He appealed to the Portuguese Government for a friendly reception. The King of Portugal owed his own throne to a successful revolt, but he was quite as much shocked by the iniquity of the English rebels as any of the longer established monarchs of the Continent. As the Commonwealth was not yet fully established, the Portuguese acted as if they thought it safe to treat it with indifference. Rupert was openly received by the king, and was allowed to make profit of his prizes. Complaints of his depredations, and outcries from the merchants trading to the Straits, whose ships were endangered by his cruisers, assailed the Council of State. In December it began to take measures to send a squadron in pursuit. Blake and Popham were ordered to consult on the measures to be taken. Almost immediately afterwards it was decided that Blake should sail alone for Lisbon, while Popham remained in the Channel. Deane had been called off for service with the army in Scotland. The squadron appointed to go with Blake was first fixed at five vessels—the Tiger, the John, the Tenth Whelp, the Signet, and the Constant Warwick. Before Blake was ready to sail, his force was increased to twelve vessels. There was, however, an interval of nearly three months between the decision to send him to the southward and the sailing of his squadron. In spite of the efforts of the New Admiralty Committee, the navy was not yet in a condition to provide large squadrons at very short notice. The calls upon its resources were many. In April of 1650 thirty-nine vessels were required in the Downs, or on the coasts of Ireland and Scotland, in addition to the twenty which were then cruising to the southward under the command of Popham and Blake. The establishment which the Council of State thought necessary was sixty-five vessels in all. Blake spent the two first months of 1650 at Plymouth, getting his squadron ready for sea. Early in March he made his appearance off the mouth of the Tagus, with a fleet strong enough to be too much, not only for Rupert, but for the feeble kingdom of Portugal. He had explicit instructions, which were confirmed and extended when Popham joined in April, to treat Rupert as a pirate, that is to say, as an enemy of the human race, who was not entitled to receive asylum. His orders were to point this out to all princes in whose ports he might meet the Royalist admiral. If they refused to take the same view, then Blake was authorised to attack Prince Rupert, even in the harbour of a State not at war with England—to act, in fact, on the principle that whoever treated Rupert as a friend was an enemy of England.

When Blake found Rupert at anchor in the Tagus, he made a demand for his surrender. A diplomatic agent was landed to represent the case of the British Parliament to the King of Portugal. King John was in a cruel position. He could not surrender Rupert without a certain amount of disgrace. Indeed he was so feeble that the Royalist adventurers would have been formidable enemies. Rupert had no scruple as to treating his host with scant politeness, and there was a party at the Portuguese Court in favour of helping the Royalists. On the other hand, the king had fair warning that if he did not treat Rupert as a pirate, the Parliament would ruin his commerce. While the king was vacillating, the two fleets remained at anchor not far from one another, and their sailors had frequent conflicts. An unsuccessful attempt was made by the Royalists to blow up Blake's flagship by a torpedo. When Blake found that the Portuguese Government was not yet ready to help him against the Royalists, he proceeded to prove to it the danger of the course it preferred. His station at the mouth of the Tagus enabled him to lay hands easily on all ships coming in or going out. When the outward-bound Brazil fleet put to sea, it was found to include several English vessels freighted by the Portuguese. These Blake pressed for the service of the Commonwealth, and sequestered their cargoes. The blow was a sharp one, and was not made more palatable by an intimation that it was only a warning, and that worse would follow if the Portuguese persisted in their ill-advised courses. The king was not unnaturally very angry, and appealed to Rupert to help him in driving off Blake's squadron. Nothing could have been more to the taste of the Royalist admiral, and if there had been any effective Portuguese fleet to help, he would have helped it. But there was not, and therefore when Rupert put to sea no battle took place. Rupert hoisted the Royal Standard and made a bold show. But in reality he could not venture to do more than skirmish with the overwhelming force opposed to him. Blake had been joined by Popham, and their combined force was not less than twenty vessels. The three capital ships and four small frigates of Rupert's own following were no match for such an antagonist. Therefore, although Rupert came near enough to have his topmast shot away, he could not venture to do much more than skirmish at a moderate distance from the forts, when the wind blew from a direction which gave him security that he could get safely back again.

Shortly after this ineffectual effort to drive off the blockading squadron, the home-coming Brazil fleet appeared, and, being quite ignorant of the state of affairs, sailed into the hands of Blake and Popham. This was a second and a worse blow to the Portuguese. Once more King John was stirred up to make an effort. Again he appealed to Rupert, and again nothing came of it. The Royalist promised help, but Blake and Popham left him no opportunity of keeping his word. Their ships by this time must have been very foul. They had good reason to be satisfied with the punishment they had inflicted on the King of Portugal, and they sailed with their prizes for the Spanish port of San Lucar de Barrameda. By this time the Portuguese Government had been taught that it was not wisdom to fight with the keepers of the liberties of England. It took advantage of the absence of Blake and Popham to get rid of Rupert, not by driving him out, a feat beyond its resources, but by bribing him to be gone. His ships were refitted, his prizes were taken off his hands, and he was bowed out. Rupert himself was not loth to be at sea again, where there were prizes to be taken. He ran through the Straits of Gibraltar and entered the Mediterranean, with the intention of preying on English commerce.

This third stage of his career began in September 1650. It was a step downwards. By this time the ruin of the Royalist cause had been put beyond doubt. The Governments of the Continent were beginning to grasp the fact that it would be wiser for them to make friends with the new power. A naval force, which no longer represented a Government in possession of even a part of its territory, was on the high road to fall into sheer piracy. It could live only by plunder, and was compelled to treat all who refused to allow it to sell its booty as enemies. In the Mediterranean, Rupert made haste to prove to all the world that he was not the man to stand upon trifles, or to consider those who were not strong enough to inspire him with respect. The extreme feebleness of the Spanish Government was a temptation to a man of his temperament. He took a bold and simple line with the Spanish authority in the southern ports. All English ships, he said, which obey the present revolutionary Government are the property of the rebels. No civilised State can be allowed to harbour such people. Therefore, when I find English ships in your harbours, I shall attack them, and, if you interfere with me, shall fire on you.

This declaration of policy was the answer of the exiled King's Lord High Admiral to the Parliament's declaration that he himself was a pirate. It was very natural, and as a matter of theory was perhaps equally accurate, but then it was not supported by the same effective force. When, therefore, Rupert insisted upon acting on the principle that his opponents were rebels, who were not entitled to enjoy asylum in the ports of foreign princes, he laid himself open to severe retaliation. As a matter of fact, he did just enough to inspire the Spaniards with a strong desire to see Blake's squadron make an end of him. At Malaga, at Velez Malaga, and again at Motril, he attacked English merchant ships, and made prize of all of them which did not run on shore, without paying the slightest respect to the neutrality of Spanish waters. Had there been any Spanish navy in existence, his career would have been short. But the Spaniards were too weak to defend themselves from insult. They were compelled to rely on the assistance of Blake, who was refitting his squadron at San Lucar, after the fatigues of the blockade at Lisbon.