Her step-father was an enemy to the cause which, from her earliest years, her heart espoused. A company of militia had been formed to assist the British Government by Sir Alexander Macdonald, the chieftain of one division of the clan, and in this regiment Macdonald of Armadale held a commission as captain, at the time when the Duke of Cumberland was "making inquisition for blood" throughout the western Highlands. But the prepossessions of Flora were unalienably engaged in favour of the exiled Stuarts; and they were not, perhaps, the less likely to glow from being necessarily suppressed. Her disposition, notwithstanding all her subsequent display of courage, was extremely mild; and her manners corresponded to her temper. Her complexion was fair; and her figure, though small, well-proportioned. In more advanced life Boswell, who with Dr. Johnson visited her, characterized her person and deportment as "genteel." There was nothing unfeminine, either in her form or in her manners, to detract from the charm of her great natural vivacity, or give a tone of hardness to her strong good sense, calm judgment, and power of decision. Her voice was sweet and low; the harsher accents of the Scottish tongue were not to be detected in her discourse; and she spoke, as Bishop Forbes relates, "English (or rather Scots) easily, and not at all through the Erse tone." In all the varied circumstances of her life, she manifested a perfect modesty and propriety of behaviour, coupled with that noble simplicity of character which led her to regard with surprise the tributes which were afterwards paid to her conduct, and to express her conviction that far too much value was placed upon what she deemed merely an act of common humanity.
In Skye, the "Isle of Mist" of the poet, she could hear imperfect intelligence of the wanderings of the Jacobite leaders. She was connected by kindred with some under whose roof the Prince had taken refuge.
The first movement which the Prince made after taking leave of Lord Lovat at Gortuleg, was to repair first to Fort Augustus, and then to Invergarie near Fort Augustus. Here he took leave of those followers who had attended him as he quitted the field of Culloden; and retained only Mr. O'Sullivan, Captain O'Neil, Captain Alan Macdonald, and one Burke, a servant. It was not until he had remained a whole day at Fort Augustus that the Prince could be persuaded that all hopes of his troops rejoining him were at an end. On Friday, the eighteenth of April, he went to Lochnargaig, where he stayed one night with Dr. Cameron of Glenkearn; and on the following day he proceeded to Oban, which is situated on a corner of Clanranald's estate. He was, therefore, under the protection of a kinsman of Flora Macdonald. He pursued his journey on the next day to the country of Arisaig, and rested at a small village called Glenbeisdale, whence he proceeded to Boradale, the place at which he had first landed in beginning the enterprise which was now terminated.