Josef Landau is a twelve-year-old boy living in Nazi Germany. On Kristallnacht, the Night of Broken Glass, seven Nazi Brownshirts (storm troopers) raid his home. Josef is dragged from his bed and thrown on the floor next to his six-year-old sister, Ruth. Josef’s father is arrested for being Jewish and practicing law. When Josef argues, the Nazis threaten to take him to a concentration camp. Josef’s mother, Rachel pleads with them, saying that he is still a boy. The family later learns that tens of thousands of Jewish men were arrested on Kristallnacht. They do not want to leave without their father. Six months later, they receive a telegram: Josef’s father has been released from the Dachau concentration camp, but the family must leave Germany within fourteen days.
Josef, Ruth, and their mother ride in the Jewish car on a train from Berlin to Hamburg. They plan to flee to Cuba, one of the few countries still accepting Jews in 1939. Josef remembers when he was forced to stand in front of his class while the teacher pointed out all of the distinguishing features of Jewish people. While his mother and sister sleep, Josef removes his paper Star of David armband and walks through the non-Jewish train cars. He buys a newspaper and has a pleasant interaction with the man who sold it, but Josef knows that the conversation would have been very different if he had been wearing his armband.
While he is trying to get a coin out of his pocket, his armband falls on the floor. A boy wearing a Hitler Youth uniform grabs the armband and makes Josef follow him to another car. Josef remembers how he was attacked by boys in Hitler Youth uniforms outside of school. One the boys was his friend Klaus. Josef knew that it was shameful for families not to have their children join the Hitler Youth, but he also knew that it turned them into monsters.
The Hitler Youth escorts Josef back to the Jewish car, bypassing a member of the Gestapo and choosing not to turn Josef in. When Josef expresses his thanks, the boy becomes embarrassed and leaves. Josef’s family arrives in Hamburg and heads to the docks, where they meet Aaron, Josef’s father. The sight of Josef’s father startles the family: his head and beard have been shaved, he is much thinner, and he is very paranoid.
While the family waits to board their ship, Josef’s father runs ahead, pushing past people in line. Josef is surprised that all of the ship’s crew, who are not wearing Star of David armbands, treat Josef and his family like normal people. Once the family is inside their cabin, which is clean and comfortable, Josef’s father tells them that it is a trick. Josef and his sister are sent to the promenade while his mother looks after his father. Josef wonders what happened to him, to change him so much.
While Josef’s mother continues to tend to his father, Josef and Ruth enjoy their time aboard the MS St. Louis: they eat proper meals and even get to watch cartoons during movie night. They make friends with two girls, Renata and Evelyne, who are Ruth’s age and play pranks on other passengers. Having just turned thirteen, Josef looks forward to his bar mitzvah, where he will celebrate becoming a man.
The first class social hall is transformed into a synagogue, and Josef has his bar mitzvah, but his father does not attend. Before the event, when one of the rabbis asked to have a portrait of Hitler removed from the social hall, the captain complied, but some of the crew were obviously angered.
Josef enjoys the bar mitzvah and wanders around the promenade. He runs into Evelyne and Renata, who are locking the doors to bathroom stalls, and reprimands them. As Josef passes by two ship stewards, he overhears them talking about the need to get to Cuba quickly, in case Cuba decides to stop accepting Jews. One of the stewards also states that Schroeder, the captain, has not told the crew everything. Joseph wonders what will happen if Cuba does not let them in.
Josef and some other children are given a tour of the ship. On the bridge, Josef asks the captain if they are racing two other boats to Cuba. The captain looks irritated, but tells Josef that there is nothing to worry about. When Josef and the other children are led to the engine room by a sailor named Jockl, they all hear another group of sailors singing “The Horst Wessel Song,” the anthem of the Nazi Party. Jockl tries to get the kids to the engine room unnoticed, but one of the singing soldiers, Schiendick, stops them. Jockl says that they have the captain’s permission to be below deck; Schiendick calls the children “Jewish rats” before letting them pass.
After hearing that one of the passengers has died, Josef’s father insists on going to the funeral, saying that he saw too many men die in Dachau without funerals. Josef attends the funeral-at-sea with his father, where they observe several Jewish traditions, including tearing their own clothes and grabbing handfuls of sand. Before the body is dropped overboard, Schiendick says that German law requires that the body be covered by the national flag. When Schiendick presents a Nazi flag to put over the body, Josef’s father spits at Schiendick’s feet. Captain Schroeder breaks up the ensuing argument and tells Schiendick to take the flag and leave the funeral. Josef notices that the captain and first officer give normal salutes as the body goes overboard, instead of Nazi salutes.
The St. Louis reaches Cuba and drops anchor a fair distance from Havana. The St. Louis is visited by a Cuban doctor who asks to conduct a medical inspection of the passengers. Josef and his family stand in line with the other passengers in the social hall, but Josef worries that his father’s mental state will get them in trouble. Josef decides that he must be the man of the family and slaps his father. He tells his father that the Cuban doctor is checking to see who should be sent back to Dachau, and Josef’s father stands at attention, just as he did when he was a prisoner. The doctor approves the passengers, but the man beside Josef says that it was just a charade. “A giant waste of time.” After the doctor leaves, several Cuban police officers block the only way off the ship and tell the passengers that they will go to Havana “tomorrow.”
Three days after the St. Louis reached Havana, two other boats with refugees are allowed to dock and then sail away. Schiendick grabs Josef and forces him to unlock his parents’ cabin, so that Schiendick and two other men can ransack the room and intimidate Josef’s parents. Schiendick spits on the floor before leaving the room, letting Josef’s father know that the visit was payback for the argument at the funeral. When Josef’s father says that Josef promised that they would not try to take him back to Dachau, Josef realizes that lying to his father during the medical inspection might have only created more problems.
Josef’s father’s confusion and paranoia increase, and he stacks furniture against the door of the cabin. Josef’s mother orders Ruthie to go to the pool and then leaves to get a sleeping draught from the doctor to give to her husband. Josef does not want to be left alone with his father. When his mother returns, she is dizzy and tired. After she told the doctor that the sleeping draught was for her (to hide her husband’s insanity), the doctor had her drink it. She falls asleep, and Josef is left to care for both his parents. Josef’s father describes to Josef how the guards at Dachau made all of the prisoners watch as they drowned a different prisoner each night. After Joseph’s father finally falls asleep, Josef goes to find Ruthie and bring her back to the cabin. When Josef returns to the cabin, his father is missing. After frantically searching the decks, he discovers that his father has jumped overboard.
There is a loud siren on the ship, and Josef yells for someone on the boat to help his father. One of the Cuban police officers removes his hat and gun and jumps overboard. A lifeboat is dropped from the St. Louis, and several boats are sent from the shore in response to the siren. The Cuban policeman helps Josef’s father into one of the shore boats, but Josef’s father struggles against them, yelling that he would rather die. The policemen subdue Josef’s father in the small boat, while Josef thinks that the man who returned from Dachau is not the father he remembers—that man is gone.
After the incident with Josef’s father, many small boats come to the St. Louis. There are reporters, people bringing food, and even family members of passengers, but none of them are allowed on board. Evelyn and Renata wave to their father in one of the small boats: he had traveled ahead of them to Cuba. When the policeman who saved Josef’s father returns to the St. Louis, Josef takes his mother and sister to the social hall to meet him. The officer, Mariano Padron, is overwhelmed by the gratitude that the passengers show him, including money. Officer Padron tells Josef’s mother that his father is alive, but sedated: he is not doing well. Officer Padron plays with Ruthie, giving her his beret and having her chase him. Initially, Josef does not want to play, but when he gives Josef his beret and then pretends to be a passenger, asking when they can go to Cuba, Josef says, “Mañana” (tomorrow). Officer Padron feels bad for bringing up the topic.
Renata and Evelyne’s father, Dr. Aber, comes to the St. Louis and takes them from the ship. The other passengers become angry, but Captain Schroeder intervenes before there is any violence. He tells the passengers that they have been denied access to Cuba and that they must leave the next day. He promises the passengers that he will try to find somewhere for them to go other than Germany, starting with a cruise along the coast of the United States. Josef asks Officer Padron about his father. Officer Padron explains that Josef’s family cannot go ashore and must leave Josef’s father, because he is not well enough to return to the ship. When the St. Louis leaves Havana Harbor, Josef tears at his shirt collar just as he had done at the funeral, to mourn the loss of his father.
From the St. Louis, Josef can see Miami on the American coast and wonders why the United States will not let them in. Most of the children still play at the pool, but the adult passengers are too defeated to socialize. Josef is surprised when his mother puts on makeup, wears a party dress, and goes to the dance hall. When he questions her, she asks him if he knows why he is named Josef. She tells him that her brother’s name was Josef, and he died in France, in the Great War (World War I). She tells Josef that he must choose to live life as a ghost, or he can dance. Josef does not understand.
There is an announcement that the St. Louis is heading back to Europe. The passengers become upset and start arguing with the crew. A man named Pozner pulls Josef aside and asks if he was one of the children that got a tour of the engine room and the bridge. When Josef tells him that he was, Pozner tells him that some of the passengers are planning to storm the bridge and force the captain to run the boat aground on the U.S. coast. Josef thinks it is a terrible plan, but Pozner tells him that they will need Josef to show them the way to the bridge.
Believing that it is his responsibility to keep his mother and sister safe, Josef has agreed to help Pozner take the bridge. Carrying metal pipes, Josef and nine other men grab the first officer, Ostermeyer, and force him onto the bridge. They surround the few officers on the bridge and make them call the captain. When Captain Schroeder arrives, he speaks calmly. He tells the ten mutineers that his crew will not take their orders, and none of the mutineers know how to steer the ship. Captain Schroeder tells them that he will forgive their attempt if they go back to their cabins and do not try again; he also promises that he will do everything that he can to take them to England. Josef feels like arguing, but the other nine men agree.
The passengers of the St. Louis celebrate, having been told that they will be divided between Belgium, the Netherlands, France, and England. Josef, his sister, and his mother are assigned to France. Josef and his family end up in Le Mans, where Ruthie goes to kindergarten and Josef gets to return to school.
Two months later, Germany invades Poland, starting World War II. Eight months after that, Germany invades France and Josef, his mother, and his sister are on the run again.
Hiding with his mother and sister in a school in Vornay, France, Josef can hear gunfire and artillery shells. When he sees a map of Europe on the wall of the classroom, he thinks about how many countries on the map have been occupied by Germany. He hears Nazi storm troopers approaching the school and leads his mother and sister to a window. After breaking the window, they climb out and run to a nearby house. However, the storm troopers chase them down, search their pockets, and find papers identifying them as Jews from Berlin. The soldiers tell them that they will be taken to concentration camps. Josef’s mother offers them money, and then diamond earrings, which she had sewn into the lining of Ruth’s jacket. The soldiers tell her that there is only enough to save one of her children. Josef realizes that the soldiers are playing a cruel game: his mother must choose whether he or Ruth has to go to a concentration camp.