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Following Edward IV’s death in April 1483 and the seizure of the throne in June by Richard, Duke of Gloucester from Edward V, Margaret was soon back at court serving the new queen, Anne Neville. Margaret carried Anne’s train at the coronation. Seeking her son’s return to England, Margaret appears to have negotiated with Richard.

Despite what these negotiations may suggest, Lady Margaret is known to have conspired with Elizabeth Woodville, mother of the two York princes whom Richard confined to the Tower of London, after rumours spread of the boys’ murder. It was at this point, according to Polydore Vergil, that Beaufort “began to hope well of her son’s fortune”.

Beaufort is believed to have initiated discussions with Woodville, via mutual physician, Lewis Caerleon, who conveyed secret correspondences between the two women. Together they conspired to supplant King Richard and by joint force replace him with Margaret’s son, Henry Tudor. Their solidified alliance further secured the subsequent dynasty by the agreed betrothal of Henry to Elizabeth of York. They hoped this proposal would attract both Yorkist and Lancastrian support.

As to the fate of the princes, it is widely held that Richard III ordered the death of his two nephews to secure his own reign. Gristwood, however, suggests that another was responsible; Henry Tudor’s path to the throne was certainly expedited by their disappearance, perhaps motive enough for his mother—his “highly able and totally committed representative”— to give the order.

Despite this suggestion, no contemporary sources corroborate the implication, whilst most contemporary accounts outline “her outstanding qualities, her courage, presence of mind, family loyalty, and a deeply felt awareness of the spiritual responsibilities of high office,” as clarified by Jones and Underwood. Before Jones and Underwood, there was no consensus within the scholarly community regarding Margaret’s role or character: historiographical opinions ranged from celebrating her to demonizing her.

It was not until the 17th century that religious retrospective speculations began to criticize Lady Margaret, but even then only as a “politic and contriving woman,” and never anything beyond shrewd or calculating. All things considered, the words of her own contemporaries, such as Tudor historian Polydore Vergil, continue to extol Lady Margaret’s noble virtues as “the most pious woman,” further removing her from accusations of wickedness.

Erasmus, in writing about his friend the Bishop, Saint John Fisher, praised Margaret’s support of religious institutions and the Bishop, further attesting the simultaneously pragmatic and charitable nature testified in the funerary sermon dedicated by the Bishop himself, as laid out in a following section.

In 1483 Margaret was certainly involved in—if not the mastermind behind—Buckingham’s rebellion. Indeed, in his biography of Richard III, historian Paul Murray Kendall describes Beaufort as the “Athena of the rebellion”. Perhaps with duplicitous motives (as he may have been desirous of the crown for himself), Buckingham conspired with Beaufort and Woodville to dethrone Richard. Margaret’s son was to sail from Brittany to join forces with him, but he arrived too late.

In October, Beaufort’s scheme proved unsuccessful; the Duke was executed and Tudor was forced back across the English Channel. Beaufort appears to have played a large role in financing the insurrection. In response to her betrayal, Richard passed an act of Parliament stripping Margaret of all her titles and estates, declaring her guilty of the following:

“Forasmoch as Margaret Countesse of Richmond, Mother to the Kyngs greate Rebell and Traytour, Herry Erle of Richemond, hath of late conspired, consedered, and comitted high Treason ayenst oure Soveraigne Lorde the King Richard the Third, in dyvers and sundry wyses, and in especiall in sendyng messages, writyngs and tokens to the said Henry… Also the said Countesse made chevisancez of greate somes of Money… and also the said Countesse conspired, consedered, and imagyned the destruction of oure said Soveraign Lorde…”

Richard did, however, stop short of a full attainder by transferring Margaret’s property to her husband, Lord Stanley. He also effectively imprisoned Margaret in her husband’s home with the hope of preventing any further correspondence with her son. However, her husband failed to stop Margaret’s continued communication with her son. When the time came for Henry to press his claim, he relied heavily on his mother to raise support for him in England.