Refugee follows the stories of three different children and their families, each attempting to flee their violent homelands, in different regions of the world and during different decades. Josef and his family flee Nazi Germany in 1938; Isabel and her family flee Cuba in 1994; and Mahmoud and his family flee Syria in 2015.

Josef Landau is a twelve-year-old boy living in Berlin. In 1938, his home is raided by Nazi storm troopers, and his father is taken to the Dachau concentration camp. Six months later, his mother receives a telegram that her husband has been released, but the family must leave Germany immediately. Josef, his sister Ruth, and his mother all travel to Hamburg to board a ship that will take them to Cuba. When Josef’s father is reunited with his family, they notice that Dachau has changed him: he is paranoid and very thin. They board the St. Louis, a large German ship, and set out.

Aboard the St. Louis, Josef’s family and the other passengers, all Jewish refugees, are treated well by Captain Schroeder and most of the ship’s crew. A few of the crew, however, openly dislike the Jewish passengers, especially Otto Schiendick, who proudly states his Nazi allegiance. When the St. Louis reaches Havana Harbor in Cuba, the ship is not allowed to dock. Josef’s father’s mental state deteriorates further, and he eventually jumps from the ship, trying to kill himself. Officer Padron, a Cuban policeman assigned to the St. Louis, saves Josef’s father. Josef’s father is taken to Havana to recover. When Officer Padron returns to the St. Louis, he is treated like a hero by the Jewish passengers. 

Eventually, the captain announces that they are not going to be allowed to dock in Havana and that the boat will be leaving. He promises the passengers that he will try to deliver them to a country other than Germany. The refugees aboard the St. Louis are delivered to England, Belgium, the Netherlands, and France. The Nazis invade France just a few months after Josef’s family arrives there. When the family is eventually caught, Josef’s mother is forced to choose which of her children will be freed and which will be sent to a concentration camp.

Isabel Fernandez is an eleven-year-old girl who lives just outside Havana in 1994. After the fall of the Soviet Union, Cuba has become inhospitable for most of its citizens under the regime of Fidel Castro. Isabel’s best friend and neighbor, Iván, is building a small boat with his father so that his family can flee to America. After a riot in Havana, Isabel’s family decides that they should also leave Cuba immediately. Isabel trades her trumpet to a fisherman for gasoline, paying her family’s way onto Iván’s family’s boat. Lito, Isabel’s grandfather, also joins them. 

The two families face many challenges as they try to cross the Caribbean Sea to Florida. A storm sweeps them to the Bahamas, where they are not allowed to disembark; Iván is attacked by sharks and eventually bleeds to death in the boat; and toward the end of the journey, Isabel’s pregnant mother goes into labor. Lito tells the story of the St. Louis and how he had to turn away so many refugees when he was a young policeman. (He is Officer Padron from Josef’s story.) Just when Miami becomes visible on the horizon, a U.S. Coast Guard boat tries to intercept the two families. Lito jumps in the water to distract the Coast Guard, and Isabel’s mother gives birth to a boy, just as they reach the shore. When Isabel is asked to play a song at her new school in America, she plays a Cuban salsa version of “The Star-Spangled Banner.”

Mahmoud Bishara is a twelve-year-old boy who lives in Aleppo, Syria in 2015. For the last few years, there has been a war in his country between the Syrian government, rebels, the Soviets, the United States and several other factions. After Mahmoud’s home is destroyed, his brother Waleed, sister Hana, and his parents drive to the border of Turkey, hoping to escape. Mahmoud’s father tells them that Germany is accepting Syrian refugees and if they can get to Greece, they will be able to travel within the European Union to reach Germany. After a violent conflict between the rebels and the Syrian government, Mahmoud and his family walk to the Turkish border. Mahmoud’s father arranges for a smuggler to take them to the island of Lesbos, in Greece. The smuggler’s raft is destroyed by rocks as they cross the Mediterranean. Mahmoud hands his sister, Hana, to another passing raft of refugees, knowing that his mother cannot hold her and swim. The family is eventually pulled from the water by the Greek Coast Guard. 

Mahmoud and his family travel through Serbia and into Hungary, where they are detained at a refugee camp that is built like a prison. Mahmoud decides that he no longer wants to be ignored and leads the refugees out of the prison, walking twelve hours to Austria. The refugees are welcomed in Austria, and Mahmoud’s family takes a train to Germany. While they travel, they ask if anyone has seen Hana. After a few weeks in Munich, Mahmoud’s family is transferred to a host family in Berlin. An elderly couple, Herr and Frau Rosenberg, welcome them into their home. Frau Rosenberg takes Mahmoud aside and tells him the story of her childhood: she is Ruth, Josef’s sister. The night that they were captured in France, Josef volunteered to be taken by the Nazis; both Josef and their mother were killed in concentration camps. Ruth promises to help Mahmoud find Hana.