In the year 1561, the young and determined Mary Stuart, portrayed by Saoirse Ronan, returns to Scotland after her husband, Francis II of France, has passed away. At just nineteen, she finds herself stepping back into a country now under Protestant rule. Her half-brother, the Earl of Moray, played by James McArdle, serves as the regent, welcoming her back to a land filled with political intrigue and danger. Having been sent to France as a child to escape death, Mary must now reclaim her throne amidst a kingdom rife with turmoil.
Across the border in England, her cousin Elizabeth, portrayed by Margot Robbie, reigns as the Protestant Queen of England. At twenty-eight, Elizabeth faces pressure from her advisors, who caution her about Mary’s claim to the English throne. The tension between the two cousins builds as Elizabeth's counsel insists that Mary should submit to her authority rather than Rome, contemplating a marriage that could secure Elizabeth's power.
Conflicts arise when Mary confronts the Protestant cleric John Knox, played by David Tennant, who views her as a threat to the Protestant cause. In a strategic move to counter Mary's potential influence, Elizabeth proposes to marry Mary to an Englishman, suggesting Robert Dudley (portrayed by Joe Alwyn), whom she secretly loves. Though both Mary and Dudley resist the idea of marriage, a bout of smallpox afflicting Elizabeth sways Mary to accept the proposition—on the condition that she is recognized as Elizabeth's heir.
In a twist of fate, Elizabeth sends Lord Darnley (played by Jack Lowden), a Catholic, to Scotland under the pretense of escaping religious oppression. Mary, wary at first, soon warms to Darnley and agrees to marry him. However, their union ignites a constitutional crisis, unsettling both England and Scotland. Elizabeth’s court voices opposition while Mary's council eye Darnley with suspicion, fearing he may elevate her claim to the throne. As tensions escalate, Darnley's actions lead to a series of betrayals and turmoil.
Upon marrying Darnley, Mary discovers him in a scandalous situation with her friend David Rizzio (Ismael Cruz Córdova). With both treachery and rebellion mounting, Mary must navigate these complications, demanding Darnley provide her with a child—a child deemed the “heir to Scotland and England,” stirring unrest among the English nobility.
As Moray conspires against her with Darnley’s father, Marquess Matthew Stewart, rumors of Mary’s infidelity circulate, fueled by Knox's fervent speeches. In a desperate turn of events, Darnley, fearing exposure of his own secrets, turns on Rizzio, whom Mary must confront. After a series of betrayals and a refusal to divorce Darnley, Mary faces mounting demands for her to abdicate the throne.
After Darnley’s death, orchestrated by forces seeking to marry Mary to the ambitious Earl of Bothwell (played by Martin Compston), she is forced into a corner. The fallout leads to further public outrage, pushing Mary towards abdication and resulting in her fleeing to England in search of support.
Upon her arrival, Elizabeth cautiously meets with her cousin. Mary implores Elizabeth for assistance in reclaiming her throne, but Elizabeth finds herself torn between her obligations and sentiments. Ultimately, fearing for her own reign, Elizabeth imprisons Mary, gathering evidence against her, leading to the tragic decision to execute her in 1567.
As Mary walks to her fate, she expresses her love for her son James (played by Andrew Rothney) and hopes for a peaceful future. In a poignant moment, Elizabeth shows remorse for her decisions, realizing the depth of their shared history. The story concludes with James ascending as the monarch of both Scotland and England, marking a significant shift in the history of both nations.
