Act One

London, 1849. A seething mass of humanity becomes visible from where they have been huddling under blankets. The Earl of Shaftesbury addresses the House of Lords about the more than 30,000 orphaned and abandoned children in the city. He claims that cholera is the best solution to the problem, having already claimed the lives of 60,000 ragged and poverty-stricken people the previous year.

In a courtroom, thirteen-year-old Joe Cooper is in the dock, accused of robbing Sir Giles Merridew. His sister, Annie, encourages him to defend himself, but Joe remains silent. The Judge says that he must have a motive to convict. The Crossing Sweeper steps forward and declares the motive as "need, cold and hunger." Annie tells the judge that she and Joe are orphans and points to Leary, also thirteen, as the true culprit. Leary denies any responsibility, and the Judge sentences Joe to seven years in the penal colonies in Botany Bay ("Music under Sentence of Judge").

At the London docks, the Patterer emerges from the crowd and sings to the health of the motley criminals ("Botany Bay"). The new transports, including Joe, arrive at the dock in chains. The ship is said to be infested with cholera, sending the crowd into a panic. The Patterer sings of the sad life of Joe Cooper ("The Ballad of Joe Cooper") as Joe makes his escape.

Annie Cooper cries in a corner at Connie Crimple's Lodging House, devastated over the loss of her brother. The other Lodgers gather. Charlie and Bill blacken their faces for the minstrel show, Alice arranges flowers as Leary sulks. Syd and Perkins arrive, back from selling cauliflower. Mrs. O'Lafferty remarks that once someone ships for Botany Bay, they're never seen again ("Now Ain't That a Blooming Shame?"). To everyone's amazement, Joe arrives at the door. Annie begs Joe to stay away from Leary from now on and asks if they can emigrate for a fresh start ("There'll Come a Day").

At Lord Shaftesbury's home, Sir Giles Merridew regales the guests with the story of his run-in with young Joe Cooper. The Aristocrats talk about how hard it is to be upper class – there are the Corn Laws to deal with, the trouble in the Crimea and, of course, the topic of what to do with the city's poor. They cheer the upper class and deride the poor, wishing that they could transport the entire lot ("Banquet Scene").

Outside, Shaftesbury is approached by the Crossing Sweeper, who gives him a look at life on the other side ("Have the Guided Tour, Sir"). The Patterer joins them as they see how the poor really live ("Roll Up"). A party of drunks appears, singing ("When We Hear That Final Trumpet"). The Crossing Sweeper shows Shaftesbury the urchin, Leary, just at the moment when he steals from a laundry girl. They see a rat fight, a group of young prostitutes, children playing at hanging each other. Connie Crimple approaches Shaftesbury and offers him a room. The poor surround them ("Deep below the City Streets").

The Crossing Sweeper and Shaftesbury arrive at the Lodging House, where Annie is coughing. Joe is concerned for her and considers going out with Leary to steal so that he can buy her food, but Annie is against it. The focus shifts as the other Lodgers joke about prostitution and cholera. Alice says that a woman from the Board of Health came in, trying to tell her how to prevent the dreaded disease ("Cholery"). Syd shows the guests a letter that he's written. Lord Shaftesbury takes it from him.

Shaftesbury reads Syd's letter to the House of Lords. It calls for attention to the plight of the poor and begs the help of the city's leaders. The others shrug it off as unimportant, but Shaftesbury stands up for the people, saying that something must be done. The Lords respond with "Let Them Starve" while the Poor beg for mercy. Lord Shaftesbury, changed by his experience, pledges the Poor his undying support.

John Giles, the cobbler, sings as he works. A group of Ragged Children join him ("Up and Be Doing / Jesus Bids Us Shine"). Giles is teaching the children how to read and write. He also gives them food. Giles seeks out Mary and asks about Annie and Joe.

At home, Lady Shaftesbury helps her young son, Francis, pack for boarding school. She asks Anthony, his older brother, to help him make a smooth transition to life at Harrow, but Anthony frightens the boy with horrible tales from school. Francis is weak and coughs terribly but insists that he will be fine. Lord and Lady Shaftesbury see him off.

Giles and the Crossing Sweeper arrive at the Lodging house to look for Annie and Joe. The Patterer and the Chorus chime in with "Be Up and Be Doing," which weaves in and out of the next few scenes. Giles is armed with "taties" and quickly convinces Annie to join his Ragged School. Annie brags that her brother is a great reader, and Giles gives Joe a new book, hoping that it will entice him to join, as well. Joe takes the book gratefully and then runs off with Leary and his gang.

At the Ragged School, Miss William plays the harmonium while the children sing ("There's a Friend for Little Children"). Joe arrives with Annie and surprises the teachers by having already read the new book – twice! The children are given fresh clothes and food to eat, but Leary arrives with his gang and wrecks the school.

Stephen Storey and his friends discuss creating the Ragged School Union. Shaftesbury offers to serve as President. Back at the school, the children practice their studies. "Rob Roy" McGregor arrives with a way for the boys to make money and help the school, as well. He suggests starting a shoeblack brigade. The boys will charge a penny a shine and split the money evenly with the school. He gives the boys badges, uniforms and shoeshine boxes ("Work, Boys, Work").

Outside, Leary teases Joe about his new uniform and tries to get him back in the gang, but Joe refuses. Shaftesbury passes by and becomes Joe's first customer. Not knowing whose shoes he's shining, Joe talks about the great Lord Shaftesbury – a saint – and admits that it's been a hard life on the street. Shaftesbury is charmed and gives Joe a sixpence.

Act Two

It seems as if all of London is off to the Great Exhibition, including the new Ragged School Shoe Black Brigade ("London Town"). Annie comes to see Joe off but is too sick to join in. Lord and Lady Shaftesbury arrive to wish the boys well, continuing on to visit Francis, who is sick in bed at Harrow. Leary and his gang are also on their way to the Great Exhibition, ready to pick the pockets of the world's elite ("London Town – Reprise")

At Harrow, the School Matron tells Lord and Lady Shaftesbury that they are too late – Francis died just thirty minutes before they arrived. A Ragged Boy appears and sings as Lady Shaftesbury breaks down ("There's a Friend for Little Children – Reprise"). The boy leaves and is replaced by Annie, wrapped in a blanket.

At Exeter Hall, Shaftesbury begs the city's leaders to do something about the condition of the poor. Holding up Annie as an example, he asks them to reach out to help save the lives of the children living in poverty.

The boys are returning from their day at the Great Exhibition, their pockets full of money ("Work, Boys, Work – Reprise"). They gather around Giles and McGregor as they count the money from the day – sixteen shillings and fourpence ha'penny! Young Sam accounts for the mysterious ha'penny – he gave a shoeshine to a one-legged man. The boys are proud of their work ("Here's to the Bootblacks"). The boys leave as Giles speaks to Joe about a revolutionary idea: The Ragged School Union has decided to help industrious children emigrate. Giles assures Joe that Annie is interested, telling Joe all about The Land of Opportunity ("Australia"). Joe will have none of it.

At the Lodging House, Annie begs Joe to reconsider. She desperately wants to emigrate and believes that Australia's sunny weather will cure her cough. Joe refuses because he doesn't think that Annie will survive the six-week voyage. Frustrated, he runs out into the night. Annie succumbs to a fit of coughing and comforted by Alice and the other Lodgers, she dies.

Lord Shaftesbury addresses the House of Lords on the subject of emigration . He notes that the State would save £100,000 a year if they sent 365 emigrants to Australia instead of 365 convicts. He is sure that the possibility of success in a new land will be the start that they need to rise up out of poverty and squalor. All they need is a chance.

In the street, Leary threatens Joe, but the Crossing Sweeper steps in just in time. Unfortunately, he bears the news of Annie's death. Refusing to believe, Joe runs back to the Lodging House. The Crossing Sweeper explains that his job is to clear the way for people. He also confronts Leary about his despicable behavior.

At the Ragged School, the children are behaving badly in the terrible heat. As the thunder rolls in, Joe appears. He knocks over desks and tables, half out of his mind with grief. Joe sinks to his knees. In a nightmare scene, Leary makes the police aware of Joe's whereabouts, then falls prey to a den of opium smokers. Joe stumbles through the streets, looking for Annie, but cannot find her. He sees Leary swinging from the gallows. A crowd appears and carries Joe over their heads. He returns and finds himself still at the Ragged School ("The Nightmare"). Joe tells Giles that he has decided to go to Australia.

In a Drawing Room, a female aristocrat sings to an attentive audience. She is joined on another part of the stage by a group of Ragged Children ("Home Sweet Home"). Joe returns to the Lodging House to pack his meager belongings. The Lodgers are excited for him to have a fresh start and sing to him, wishing him well ("The Ballad of Joe Cooper – Reprise").

At the docks, the scene is a far cry from the first time that Joe was to ship out. A spirit of excitement is in the air as the crowd bids farewell to the emigrants. Joe says goodbye to Giles, McGregor and Shaftesbury, and boards happily, but an Officer appears and points Joe out to a Policeman ("The Voyage"). At sea, the ship is caught in a violent storm but finally arrives in Australia, where everyone is promised a fresh new start.

Giles and Shaftesbury wonder about the boys whom they have sent overseas. They have heard good news from many but have yet to hear from Joe Cooper. They believe that, out of all of the boys, Joe will be the one to make his mark.

When Joe steps off the boat at Port Adelaide, he is arrested by Police Officers who accuse him of fraud and trying to escape punishment. They sentence him to seven years in prison. A Judge asks Joe if he has anything to say for himself. Joe remains silent and accepts his punishment as the inmates surround him and pull him back into the mire.