In addition to providing a substantial number of men to Montrose's cause, Badenoch experienced the devastation resulting from a succession of armies passing through it during the era 1644-54. Montrose's force passed through at least twice pursued by the Marquis of Argyll and General Bailie. Armies in those days didn't have supply trains; they lived off the land and took what they needed from the local population. Often they laid waste to what they couldn't carry with them to deprive the enemy of this source of supply.
After his defeat at Philiphaugh, Montrose tried to recruit another Royalist force in the Highlands but the Marquis of Huntly's jealousy kept the Gordons from joining him and achieving an effective force. When Montrose obeyed the King's orders to disband in 1646 and left Scotland for European exile, Huntly then decided to carry on the fight but the Scots army delivered the King to the English in January 1647 and returned to Scotland to deal with Huntly. As Leslie approached, Huntly fled to Lochaber leaving Leslie to reduce Huntly's castles systematically. One of these was Ruthven.
Leslie then marched to Kintyre to deal with the Irish MacDonalds who had reconstituted there after Philiphaugh. As Leslie approached, the MacDonalds moved to Islay but Leslie pursued them there and to other Hebridean islands. His force was made up of a substantial number of Campbells who relished the opportunity to take advantage of the opportunity to add to their holdings. While this campaign was progressing another Covenanting force pursued Huntly who had been hiding in Lochaber and finally captured him in December 1647. Huntly was imprisoned at Edinburgh but wasn't executed despite Argyll's urgings. He sought possession of Huntly's lands and, had he succeeded, would have been the Macphersons' superior.
Ruthven Castle was recaptured by Thomas Mackenzie of Pluscardine, a Royalist who had joined a rising by several Highland clans in February 1649. The first attack was against Inverness which was captured and its fortifications demolished. Pluscardine then marched into Badenoch and took the castle from the Covenanter garrison. General Leslie came north again to deal with the rising and restored the Castle to control by the Scottish parliament. The record indicates that this time the Macphersons were on the Parliament's side because they received payment of £500 Scots "in consideration of their losses caused by the invasion by the laird of Pluscardine." The following year, "thirty men of the Marquis of Argyll's regiment were appointed to be left" there.
With the English occupation of Scotland in 1652, Ruthven Castle was among the fortresses garrisoned by them. In 1653, the Earl of Glencairn rose in support of King Charles II and although the insurgents operated in Badenoch, Ruthven Castle did not change hands. However, General Monck did march into Badenoch and visited the Castle in July 1654 while pursuing the Royalists into Lochaber.