The HMS Pinafore lies in anchor at Portsmouth harbour. Onboard the crew sings of their life on the ocean wave as they set about their daily routine. Their work is soon interrupted by the arrival of Mrs Cripps, a local bumboat woman, (known affectionately by the men as Little Buttercup) who has come to sell whatever she can from her basket. She is struck by the melancholy appearance of one of the sailors, Ralph Rackstraw, whose name, when she learns of it, troubles her. We learn that Ralph has fallen in love with Josephine – daughter of the ship’s commanding office, Captain Corcoran – a lady so far above his social station as to make his suit hopeless.

The captain appears on deck and compliments the crew, yet when the sailors depart, reveals to Buttercup that he is deeply troubled. His daughter is being sought in marriage by Sir Joseph Porter, the First Lord of the Admiralty, but for some reason she does not take kindly to this match. After Buttercup departs Josephine arrives and admits her reluctance to be courted by Sir Joseph is due to the fact that she is in love with someone else. Because the object of her affection is but a lowly sailor onboard HMS Pinafore she assures her father that she will never pursue a liaison with one so ignobly born. Sir Joseph arrives on board attended by his cousin Hebe and an entourage of adoring sisters, cousins and aunts, proud of his rise from humble office boy to his present exalted position. He proceeds to inspect the ship’s company but finds the Captain’s manner in delivering orders to the men somewhat discourteous. They are, as Sir Joseph says, any man’s equal – excepting this.

After the crew has departed Josephine arrives on deck to meet Ralph, who has resolved to declare his feelings for her. Although she loves him too she forces herself into a show of outrage and disdain. Distracted, Ralph sees suicide as his only course and conveys his resolution to his shipmates. Appalled, they stand back as he raises a pistol to his head. Suddenly Josephine, who cannot stand by and watch this happen, bursts on deck and declares her love for him. Given the obstacles to their union they plan to elope although Dick Deadeye, a fellow sailor hated by all the crew, warns them against this folly. Not in the mood for his misanthropic utterances, everyone’s high spirits soon return.

It is night and Buttercup, who is asleep on deck, is secretly approached by Cousin Hebe, who explains a plan that will resolve the romantic difficulties of everyone on board. Buttercup in earlier days had been foster mother to two little boys of widely different backgrounds. Somehow the two babies had been mixed up and that the more privileged infant was in fact Ralph Rackstraw. Hebe suggests a fabrication that the other child, present identity unknown, grew up to be none other than Captain Corcoran. Hebe withdraws and the Captain appears and soliloquises to the moon about his troubles. Buttercup overhears this and offers a sympathetic ear, but despite their reciprocal feelings differences in their social positions make anything more than friendship out of the question. In response Buttercup prophesises a change for the Captain – for things are seldom what they seem.

Sir Joseph meanwhile has been pressing suit with Josephine with little success. Corcoran, anxious to please the First Lord, suggests that his daughter may be dazzled by his exalted position and that he would do well to assure her that love is a platform on which all ranks can meet. The two men retire, as Josephine appears onstage and alone expresses her misgivings regarding the elopement she is about to take. Sir Joseph joins her and, acting upon the Captain’s suggestion states his belief that love levels all ranks. This statement removes all Josephine’s previous misgivings and Sir Joseph, unaware of how strongly he has pleaded his rival’s case, believes her positive response a sure sign of his success. The Captain is pleased at the prospect of marriage between his daughter and cabinet minister, although this is short lived as Dick Deadeye appears revealing their plans for elopement.

The captain lies in wait as the lovers, assisted by Buttercup and the crew, appear on deck. They are about to leave the ship when the Captain steps out from hiding and, incensed by Ralph’s presumption that he cannot control his tongue exclaims ‘Why damme, it’s too bad!’ Sir Joseph who has come to investigate all the commotion appears and, shocked at his language, dismisses the Captain to his cabin in disgrace and orders Ralph away for his involvement with Josephine. Buttercup reveals the error that has long troubled her conscience and events make it imperative that the truth be known. Sir Joseph orders Ralph and Corcoran before him who appear dressed in the others social dress. With the tables turned Sir Joseph looses all interest in marrying Josephine, the daughter of a sailor and resigns himself to a union with Hebe. Ralph and Josephine and Corcoran and Buttercup finally unite.