Mary Stuart is imprisoned in England—nominally for the murder of her husband, Darnley, but actually because she has pushed her claim to the throne of England currently held by her cousin, Queen Elizabeth I. Even though Elizabeth ordered Mary’s imprisonment eighteen years ago, she hesitates over signing her death sentence. She realizes that even though Mary, a Catholic, is a threat to her Protestant throne, it may be even more dangerous to execute her, because of Mary’s many friends and allies in Scotland and France. Mary, of course, hopes for a reprieve.
Mary soon learns that Mortimer, the nephew of one of her guardians, has converted to Catholicism and is secretly working with her French friends for her release. This is a dangerous situation for Mortimer, but may be Mary’s only hope to avoid the scaffold.
During all this, some of Elizabeth’s advisors are divided on how to deal with Mary. Lord Burleigh, the high treasurer, tells Mary the execution should be carried out; the Earl of Shrewsbury feels that the law has not been fairly applied; and the Earl of Leicester, who secretly supports Mary and has joined with Mortimer, says the sentence should stand, but that there is no need for her to die immediately. But, this is only some of the intrigue. Queen Elizabeth, herself, has also been scheming to somehow have Mary executed or murdered without the blame falling on her.
To complicate matters further, Leicester is afraid his duplicitous support of Mary is about to be discovered. To reestablish his own reputation, he has Mortimer seized as a traitor. To avoid incriminating Mary, Mortimer kills himself in the arms of the guards.
Leicester, to even further move suspicion away from himself, declares that Mary should die. He is sorely surprised, however, when Elizabeth instructs him to carry out the execution—to clear away any lingering doubts concerning his allegiance.
A mob is in the street clamoring for the execution of Mary Stuart. Burleigh and William Davison, the secretary of state, bring Elizabeth the death warrant to sign, but she is still apprehensive. She considers the pressures on her from her people to execute Mary and from France, Spain, and the Pope, to spare her life. She decides she can only be free when Mary is dead and signs the warrant. She returns the death warrant to Davison, but is purposely ambiguous about whether he is to hold the document or to have the execution carried out. Burleigh takes the warrant from him, with plans to carry it out.
Mary, upon hearing of the impending execution, receives communion, makes her final requests, and scornfully takes leave of Leicester.
Elizabeth, meanwhile, awaits news, exalting that Mary will soon be dead. Once the execution is completed, Mary transfers the burden of responsibility to Burleigh and Davison. She banishes Burleigh from her presence for not conferring with her about it, and she has Davison sent to the Tower. Leicester has secretly left for France.
In short, Elizabeth is victorious and secure, but now utterly alone.