In 1561, Mary Stuart (Saoirse Ronan), the young Catholic Queen of Scotland, returns to her homeland after the death of her husband, Francis II of France. At just nineteen, Mary is met by her half-brother, the Earl of Moray (James McArdle), who serves as the regent of Scotland. To escape potential death at home, Mary had been sent to France as a child, but now she steps back into a politically charged environment dominated by Protestant influence.
Meanwhile, in England, Elizabeth I (Margot Robbie), now twenty-eight and still single, faces the looming threat of Mary's claim to the English throne. Her advisers warn her that Mary must yield to her authority, and they plot to secure Elizabeth's reign by marrying Mary off to an English noble. Among the candidates is Robert Dudley (Joe Alwyn), with whom Elizabeth harbors secret affections. Reluctantly, Mary contemplates a marriage to Dudley but demands that her position as Elizabeth's heir is secured.
In a twist of fate, Lord Darnley (Jack Lowden), a Catholic noble, is sent to Mary under the guise of seeking refuge from persecution. Although Mary is initially suspicious, she grows fond of Darnley, leading to a marriage proposal that triggers a constitutional crisis in both Scotland and England. Concerns swirl around the implications of this union, as Darnley's noble status could elevate Mary’s claim to the English throne. Tensions rise when Darnley's presence ignites animosity within Elizabeth’s court, while in Scotland, Mary's council casts a wary eye on him, fearing an English takeover.
As Darnley and Mary unite, their marriage is marred by scandal when Mary unexpectedly finds Darnley entangled in a compromising situation with her close confidant, David Rizzio (Ismael Cruz Córdova). In a gripping showdown, Mary decides to take action against the growing rebellion, yet she spares both Rizzio and Moray, asserting her will in a turbulent time. As Mary's prospects for a child loom, she declares the baby to be heir to both Scotland and England, a proclamation that stirs deep resentment among the English.
In a web of betrayal, Matthew Stewart (Brendan Coyle), 4th Earl of Lennox and Darnley's father, aligns with Moray to undermine Mary’s rule, spreading malicious rumors of her infidelity. Faced with mounting pressure, Darnley is reluctantly drawn into a plot to eliminate Rizzio, leading to tragic consequences. Despite the chaos, Mary seeks reconciliation, inviting Elizabeth to be the godmother of her unborn child.
However, personal vendettas and political ambitions intertwine, leading to Darnley's banishment and culminating in his mysterious murder instigated by Earl of Bothwell (Martin Compston). As Darnley’s death spirals into a public relations disaster, Mary is labeled a harlot, inciting calls for her abdication. Reluctantly, she relinquishes her throne, seeking refuge in England.
Upon her arrival, Elizabeth agrees to a secret meeting where Mary pleads for support to reclaim her heritage. Yet, Elizabeth's hesitance—rooted in fear of a Catholic uprising—leads to Mary's imprisonment. The unfolding events culminate in a life-altering decision for Elizabeth, forced by political necessity to order Mary's execution in 1567.
As Mary walks toward her fate, a remorseful Elizabeth dons a vivid red dress, reflecting the gravity of what they have lost—sisters by blood, queens by destiny. In her final moments, Mary expresses hope for her son, James (Andrew Rothney), and a longing for peace within the realms. A poignant postscript reveals James rising to power, becoming the first monarch to unite both Scotland and England after Elizabeth’s death in 1603.
