Monck's march south and the return of the long parliament brought Edward Montagu, future earl of Sandwich, to the position of commander at sea and it was his fleet that, after some frantic woodwork to recreate the ships’ royal arms, set off to return the king to his kingdoms. In Old Aberdeen the minister, Alexander Scrogie, told students that without a king Scotland had been ‘as a Ship without a Pilot and Helmn, tossed with tempestuous and stormy winds and waves among rocks and shelves, or pursued by Pirates’. The new helmsman certainly enjoyed that role, in a literal sense, for he loved sailing and the navy was both his instrument and passion.

Within a few years the actions of Charles II's captains in Africa and America, and his pretensions to sovereignty of the British seas, had driven his sometime refuge to war. Cromwellian veterans were confident that having comprehensively beaten the Dutch once, they could easily repeat the feat, binging both profit and prestige to the monarchy. Charles's brother James, duke of York, commanded the first battle of the war, at Lowestoft (3 June 1665). In a duel of flagships, a shot felled a group of gentlemen standing by the duke, but the Dutch Eendracht – union, for that of the seven provinces – exploded with such force that it was heard in the Hague. James's close shave draws some speculation. If there had been no King James VII could there have been parliamentary union in 1707 without the proximate threat of a Jacobite restoration? The risk to his brother aside, the war against one of Scotland's closest trading partners and fellow calvinists could have subjected Charles's union to Eendracht's fate.

Only the second foreign conflict conducted under the auspices of regal union, the Dutch wars were more directly against Scottish interests than Charles I's Spanish war, but how the navy operated had something to commend it to Scots, and actually bears some comparison to what the Covenanters had wanted of the navy. Scottish accounts of the Dutch wars sometimes present them as an unrelieved negative, with the considerable damage to trade and the burden of a levy of seamen for the royal navy detailed.