Mary's situation outside the castle walls was urgent—she was a young queen in remote country with a comparatively small entourage, facing an open challenge from one of the most powerful noble houses in Scotland. Word of her predicament spread quickly through the Highland clans. George Buchanan, who wrote the earliest surviving account, names the Frasers and the Munros as the clans that rallied to her: 'Upon hearing of the danger of their princess, a great number of the ancient Scots, partly by persuasion, and partly of their own accord, flocked around her, particularly the Frasers and Monros, the bravest of these tribes.' Alexander Mackenzie's much later history adds the Mackenzies and the Rosses to the muster, but Buchanan's contemporary account—written in Latin and translated by James Aikman in 1827—names only the two clans, and his is the version closer to the events.

The castle's garrison was thin. Records put it at only 12 or 14 'able persons'—a token defence force, perhaps reflecting Alexander Gordon's expectation that Mary would not be in a position to press a siege. Once the loyal clans had assembled, the besieging force significantly outnumbered the defenders. The fortifications themselves were not adequate for sustained resistance. Buchanan's summary is direct: 'When the queen found herself sufficiently strong, she laid siege to the castle, which having neither a sufficient garrison, not being properly fortified for sustaining an attack, surrendered, when the commanders were executed, and the men dismissed.' Most of the garrison were allowed to walk free. Alexander Gordon and a handful of key officers were imprisoned. Gordon himself, as the man who had ordered the gates closed, was hanged for treason.

The English diplomat Thomas Randolph was at Inverness during the siege and recorded the Queen's mood. Mary was twenty years old. Her cousin Elizabeth Tudor sat on the English throne and would not meet her face to face. She had been raised in France, returned to Scotland barely a year earlier, and was now in the Highlands directing what amounted to a small war against one of her own earls. According to Randolph, she 'was in high spirits and undismayed in the conflict.' When the night watch returned in the morning, Mary made a remark Randolph thought worth recording: she regretted that she was 'not a man to know what life it was to lie all night in the fields, or to walk upon the causeway with a jack and knapschall, a Glasgow buckler and a broad sword.' The jack was a quilted defensive coat; the knapschall a helmet; the buckler a small round shield. Mary wanted to be in the watch with her soldiers.

Mary's expenses while in Inverness, recorded in the accounts of her household, include gunpowder—an entry that confirms the practical military side of the operation—and 15 tartan plaids purchased for her lackeys and members of her household. The tartan purchases are revealing. Highland dress was not yet the romantic costume it would become in the 18th and 19th centuries, but it was distinctively Scottish, and Mary, having spent her formative years in the French court, was demonstrating that she belonged in the Highlands as much as in the Privy Council in Edinburgh. The fall of Inverness Castle was the prelude to a broader campaign against the Earl of Huntly. The Earl had backed his son in defying the Queen, miscalculated the political consequences, and within weeks would be dead—reportedly of stroke or apoplexy—at the Battle of Corrichie outside Aberdeen on 28 October.

Alexander Gordon's severed head went up on the castle wall as a public warning. The display followed the standard practice of the era for executed traitors—the heads of high-profile prisoners typically remained on view for weeks or months, visible to the townspeople and to anyone arriving on the river. The castle that Alexander Gordon had defended would not survive the next century in its 1562 form; the present Inverness Castle, the sandstone building on Castle Hill, dates largely from 1836. But the rocky promontory above the River Ness has held a fortification almost continuously since at least the 11th century. Mary Stuart's three-day siege there is one chapter in a story that includes Jacobite rebellion, Hanoverian destruction, Victorian reconstruction, and—most recently—the building's reopening as a Highland visitor attraction. The Earl of Huntly's defiance was over within weeks. The fortress remains.