In 1585, Catholic Spain, ruled by King Philip of Spain (Jordi Mollà), is the most powerful country in the world. Seeing Protestant England as a threat, and in retaliation for English piracy of Spanish ships, Philip plots to take over England and make his daughter, Isabella, the Queen of England in Elizabeth's place. Meanwhile, Queen Elizabeth Tudor I (Cate Blanchett) of England is pressured by her advisor, Francis Walsingham (Geoffrey Rush), to marry - if she dies childless, the throne will pass to her second cousin, Mary, Queen of Scots (Samantha Morton), who is Catholic.
English explorer Walter Raleigh (Clive Owen) is presented at Queen Elizabeth's English court, having returned from the New World. Queen Elizabeth is attracted to Raleigh, enthralled by his tales of exploration, and asks Bess Throckmorton (Abbie Cornish), her most favored lady-in-waiting, to observe him. Bess also finds Raleigh attractive and they begin a secret affair. With tensions strained between England and Spain, Elizabeth seeks guidance from her astrologer, Dr. John Dee.
Jesuits in London conspire with Philip to assassinate Queen Elizabeth and replace her with Queen Mary, in what King Philip calls "The English Enterprise", historically known as the Babington Plot. From her imprisonment, Queen Mary sends secret correspondence to the Jesuits, who recruit Anthony Babington to assassinate Elizabeth. Walsingham continues to warn Queen Elizabeth of Spain's rising power and of the Catholics' plots against her, but unlike her predecessor and half-sister Mary I of England, Elizabeth refuses to force her people to share her religious beliefs.
Walsingham's Catholic brother, who knows of the plot against Elizabeth, is jailed, leading Walsingham to reveal Spain's plan to Queen Elizabeth, who angrily confronts the Spanish diplomats. The Spanish ambassador feigns ignorance, accuses Queen Elizabeth of receiving Spanish gold from pirates, and insinuates that she has a sexual relationship with Raleigh. Enraged, Elizabeth throws the Spaniards out of court. Meanwhile, Philip is cutting down the forests of Spain to build the Spanish Armada to invade England. Mary writes letters condoning the plot.
Babington storms into a cathedral where Elizabeth is praying and fires a pistol at her, though Elizabeth is unharmed as there was no bullet in the gun. As Elizabeth learns of Mary's involvement in the plot, Walsingham insists Mary be executed to quell any possible revolt. Elizabeth reluctantly agrees. Mary is tried for high treason and beheaded; Walsingham realizes this was part of the Jesuits' plan all along: Philip never intended for Mary to become queen, but with the Pope and other Catholic leaders regarding Mary as the true Queen of England, Philip uses Mary's death to obtain papal approval for war. The "murder" of the last legitimate Catholic in the line of succession gives Philip the pretext he needs to invade England and remove Elizabeth, leaving the way to the English throne free for his own daughter.
Bess reveals to Raleigh that she is pregnant with his child, and pleads with him to leave. Instead, the couple marries in secret. When Elizabeth confronts Bess, she confesses her pregnancy and that Raleigh is her husband. An infuriated Elizabeth berates Bess, reminding her that she cannot marry without royal consent. She banishes Bess from court and has Raleigh imprisoned for the crime of seducing a ward of the Queen.
As the Spanish Armada begins its approach up the English Channel, Elizabeth forgives Bess and sets Raleigh free to join Sir Francis Drake in the battle. The ships of the Armada vastly outnumber England's, but a storm blows the Armada toward the beaches, endangering its formation and becoming vulnerable to English fire ships. Elizabeth, atop her coastal headquarters, walks out to the cliffs and watches the Spanish Armada sink in flames as the English prevail.
She visits Raleigh and Bess and blesses their child. Elizabeth appears to triumph personally through her ordeal, again resigned to her role as the Virgin Queen and mother to the English people.
Cate Blanchett as Queen Elizabeth I
Geoffrey Rush as Sir Francis Walsingham
Clive Owen as Sir Walter Raleigh
Abbie Cornish as Bess Throckmorton
Samantha Morton as Mary, Queen of Scots
Jordi Mollà as King Philip II of Spain
Susan Lynch as Annette Fleming
Rhys Ifans as Robert Reston
Eddie Redmayne as Anthony Babington
Tom Hollander as Amias Paulet
David Threlfall as John Dee
Steven Robertson as Sir Francis Throckmorton
Adam Godley as William Walsingham
Laurence Fox as Sir Christopher Hatton
William Houston as Guerau de Espés
Christian Brassington as Charles II, Archduke of Austria
John Shrapnel as Charles Howard, 1st Earl of Nottingham
Kelly Hunter as Ursula Walsingham