Prince Rupert at Kinsale, 1649
Prince Rupert's flagship when he sailed from Helvoetsluys was the 40-gun Constant Reformation. Her captain was the Royalist veteran Richard Fielding. Rupert's vice-admiral was his brother Prince Maurice in the 40-gun Convertine, whose captain was Elias Jordan. His rear-admiral was Sir John Mennes in the 36-gun Swallow. Other ships in the squadron were the Guinea (30 guns) commanded by Captain Thomas Allin, which was sometimes called the Charles; the 34-gun James, the Thomas, the ketch Mary and the hoy Elizabeth. Two other ships, the Roebuck (14 guns) commanded by Captain Phillip Marshall and the Blackamoor Lady (18 guns) commanded by Captain Dossey had already put to sea to search for prizes, with orders to rendezvous with the squadron off the Isles of Scilly. Three large Dutch Indiamen also sailed with the squadron for protection from pirates and privateers.
During the voyage down the English Channel, the Royalists drove off Vice-Admiral Moulton's squadron near Dover and captured five merchant ships as prizes. Shortly after his arrival at Kinsale, Prince Rupert learned of the execution of his uncle King Charles I and the declaration of the Commonwealth of England. Rupert swore vengeance on the regicides, whom he regarded as murderers. Despite the difficulties of communication between The Hague and Kinsale, Rupert received his formal commission as admiral and lieutenant-general of Charles II's naval forces in March 1649.
Rupert sold the prizes taken in the Channel and used the funds to begin recruiting crews and fitting out his ships for service as privateers. By the middle of March 1649, Rupert had sent out four ships under the command of Sir John Mennes to take prizes and to establish contact with Sir John Grenville in the Isles of Scilly. Mennes took five prizes, one of which was taken into Rupert's squadron as the Scott (30 guns), the rest were sold at Kinsale. Although several more prizes were taken, two of Rupert's ships, the Guinea and the Thomas were captured in April by Moulton's squadron, which had been ordered to patrol the Western Approaches while the Commonwealth navy prepared a larger fleet to sail against Rupert.
Having concluded the Second Ormond Peace in January 1649, the Marquis of Ormond wanted to use Rupert's squadron in support of his military campaign in Ireland. During the early part of the year, however, both Ormond and Rupert were making preparations and were not ready to co-operate. By late spring, Ormond had begun to move against the isolated Commonwealth enclaves in Leinster and Ulster and wanted Rupert's squadron to blockade Dublin while he besieged the city by land. However, the Commonwealth navy moved quickly to secure the sea routes between Dublin and the British mainland. Around the middle of May 1649, the Irish Sea squadron, consisting of four powerful warships under the command of Sir George Ayscue in the Andrew, arrived off Dublin. At the same time, the newly-appointed generals-at-sea Robert Blake, Richard Deane and Edward Popham sailed from Plymouth with a fleet of ten warships. The generals arrived off Kinsale on 22 May to blockade Rupert's squadron in the harbour and to keep watch on the Irish privateering ports of Wexford and Waterford. When the blockade was established, the generals separated. Popham returned to the Downs, Deane concentrated on preparations for conveying Commonwealth troops to Ireland, leaving Blake in his flagship the Triumph (62 guns) to command the blockading squadron.
After consultation with his captains and correspondence with Ormond, Rupert decided against attempting to fight Blake. Instead he fortified the mouth of Kinsale harbour with gun batteries and concentrated on refitting his ships and recruiting crews from the southern Irish ports. His intention was to escape with his best ships fully-manned to continue privateering operations from a more secure base. During the summer of 1649, the Royalist cause in Ireland suffered a major setback with the defeat of Ormond's field army at the battle of Rathmines outside Dublin in early August. This was followed two weeks later by the landing of the Commonwealth invasion force under the command of Oliver Cromwell. After storming Drogheda in September, Cromwell's army marched south from Dublin to capture Wexford the following month. As well as the relentless advance of Cromwell's forces from the north, Rupert's position was threatened by the break-up of Ormond's coalition as Irish Protestants began to defect to the Commonwealth. The ringleader of a plot to betray Kinsale was hanged on Rupert's orders. Rupert also had a narrow escape when he declined an invitation to go on a hunting expedition with the governor of Cork, who planned to take him prisoner before declaring for the Commonwealth on 16 October.
By the end of September 1649, only five of Blake's blockading squadron remained on station. The rest were either in port for refitting, supporting Cromwell's forces or on escort duty. When a deterioration in the weather in mid-October forced Blake's remaining ships to seek shelter in Milford Haven, Rupert took the opportunity to escape from Kinsale with his seven best ships, leaving the James and the Roebuck which were later seized by Commonwealth forces.
John Barratt, Cromwell's Wars at Sea (Barnsley 2006)
Bernard Capp, Cromwell's Navy, (Oxford 1989)
S.R. Gardiner, History of the Commonwealth and Protectorate vol. i (London 1903)
Frank Kitson, Prince Rupert, admiral and general-at-sea (London 1998)
Eliot Warburton, Memoirs of Prince Rupert and the Cavaliers vol iii (London 1849)
Royalist vessels of the English Civil Wars and Commonwealth 3decks naval warfare wiki