Act One

The Prologue begins with a silhouette of a woman at the wheel of a ship. She is Grace O’Malley. When the curtain rises we see that she is a young woman, merely pretending. A young man enters, and Grace hides from him. He is Tiernan, her childhood friend. They begin to swordfight until they get too close. They begin to kiss passionately.

The musical opens in Clew Bay, on the launching of Clan O’Malley’s newest ship, The Pirate Queen, captained by Chieftain Dubhdara O’Malley ("The Pirate Queen"). We see Grace, Chief Dubhdara’s daughter, who begs to be allowed to be a sailor on the Pirate Queen’s maiden voyage. When he denies her, she laments to Tiernan about the restraints of being a woman during this time ("Woman"). At a time when women on a ship are considered to bring bad luck, she decides to hide among the crew disguised as a boy. When disaster subsequently strikes on the high seas, she proves her mettle and earns her place as one of the ship’s crew ("My Grace").

Ecstatic that she can stay on board, Grace and Tiernan promise each other that they will marry ("Here On This Night"). Clan O’Malley goes about its business of pirating the seas and encounters the British War ship. During this battle Grace shows her bravery and leadership when she single-handedly saves her fathers life, and kills the English Captain. This action causes Dubhdara to decide to make her the captain of the Pirate Queen. He says, “You, Grace, are the Pirate Queen”. Grace becomes famous and feared as a proud defender of her country. In England, Queen Elizabeth I rises to start a new day ("The Waking of The Queen"). She and her confidante, Lord Richard Bingham, weigh the news of this formidable woman. Elizabeth considers herself Queen of Ireland and will have no rival, least of all a woman! She orders Grace O’Malley destroyed ("Rah-Rah, Tip-Top").

Ireland finds itself in turmoil. As England’s oppression grows, warring Irish clans are forced to unite. Clans O’Flaherty and O’Malley meet and decide to join together. Although Grace is still in love with Tiernan, she is to be married to Donal O’Flaherty, heir to Clan O’Flaherty, as a way to unite the clans. Tiernan is heartbroken at the news. Grace is equally devastated that she must give up everything she has fought for: Tiernan and the Sea ("The Choice Is Mine"). Nevertheless she accepts it as her duty to her country, and accepts the marriage union. Donal brags to the men of Clan O'Flaherty that he'll tame his new bride (Boys'll Be Boys). She and Donal are married ("The Wedding"). Tiernan soliloquises on his continuing love for Grace, and vows to always be her protector ("I'll Be There").

Donal proves himself to be a womanising, cowardly scoundrel and his marriage to Grace is a stormy affair. About a year into their marriage, the English attack Rockfleet, where Grace and the rest of the Clan O’Flaherty reside, while the men were off fighting in Belclare. The women, led by Grace, defeat the English soldiers by seducing them and then killing them. However, we find out that the English also attacked Clew Bay and that Dubhdara was badly wounded by an English blade, and Grania, Donal, and the clan travel to see him before his death ("A Day Beyond Belclare"). Meanwhile, Bingham returns to England, defeated and in disgrace.

On his deathbed, Dubhdara names Grace as his successor, despite the fact that she is a woman. As Dubdhara dies, Grace accepts her new role as Chieftain of the Clan O’Malley ("Sail To The Stars").

Act Two

Amidst continued war with the English, Grace gives birth to a son, Eoin ("Enemy At Port Side"). Donal’s cowardice in one crucial battle proves the breaking point for Grace. In the tradition of the Brehon Law, she “dismisses” him publicly, officially dissolving their marriage ("I Dismiss You"). Tiernan and Grania privately reflect on their feelings for each other and in the end kiss and reunite ("If I Said I Loved You").

Lord Bingham suggests to Queen Elizabeth that she may marry the man who defeats Ireland, allowing them to produce an English heir ("The Role of The Queen"). Bingham becomes determined to bring down Grace O’Malley once and for all. Emasculated and shamed, Donal colludes with Lord Bingham, betraying the Clan O’Malley and Ireland itself.

Eoin is christened ("The Christening"). The celebration is interrupted by Donal, asking to be with his son ("Let A Father Stand By His Son"). But it's a distraction - Clew Bay is invaded. Grace is arrested. In the melee, Tiernan kills Donal and escapes with Eoin.

Grace is jailed, and all of the other Irish Chieftains surrender their crowns to England. Tiernan, whose feelings for Grace have never changed, offers the English a trade - his freedom for Grace’s ("Surrender"). Elizabeth finds herself affected by this turn of events and she grants Tiernan’s request. She reflects on her own life as a woman in power, as Grace, locked in prison, reflects on her life in shambles. They both conclude that it is a woman in love who has all ("She Who Has All"). Grace is freed to care for her child, and Tiernan is imprisoned in her place. Reunited with her child, Grace’s joy is tempered by the realisation of how Ireland has changed during her imprisonment. The country has grown desolate, her lands are ravaged, her people are hungry, and injustice reigns.

Grace takes fate into her own hands and returns to England to confront Queen Elizabeth ("The Sea Of Life"). Granted an audience, these two powerful women - one reigning queen and another without a crown - find themselves face to face, in a private conversation unheard by eager courtiers ("Woman to Woman"). The most unexpected truce is hammered out between them, freeing Clew Bay from the worst of English rule. Tiernan is granted his freedom and Lord Bingham falls into disgrace.

Grace and Tiernan find themselves reunited at last ("Finale"). Unencumbered now by war and previous alliances, they can finally pledge themselves to each other and pray for extended peace in Ireland.