Number the Stars is a historical novel set in Denmark during World War II. Lowry has written the novel in third person ("He says," as opposed to, "I said," which is first person), using a limited omniscient viewpoint (only Annemarie's thoughts and feelings are revealed). Ten-year-old Annemarie Johansen and her family live in Copenhagen, Denmark. Their lives have changed drastically because the Nazis now occupy Denmark (1943). Through Annemarie, we learn that the Danes must abide by curfews and use blackout curtains on their windows. They have no fuel for heat, and electricity has been rationed. The Danes must use candles to light their homes. They have sadly become accustomed to Nazi soldiers standing on every street corner and have learned to be "just another face in the crowd," going about their business, trying not to be noticed by the Nazis. The adults are fearful and sad because they understand the dangers of the Nazis occupation of Denmark and they have experienced loss resulting from the actions of the Nazis. Annemarie's older sister, Lise, was killed because she was an active member of the Danish Resistance, a group of people opposed to the Nazi occupation of Denmark and supportive of the Danish Jews. Annemarie, her five-year-old sister, Kirsti, and her best friend, Ellen Rosen, are unaware of the danger that surrounds them. They are only aware of obvious changes that have affected their lives. They are aware of the food shortages (sugar is no longer available, they eat bread without butter, and their mothers drink "coffee," which is really just herb-flavored water); they can't get rubber tires so bicycles have wooden wheels; they are unable to get leather shoes — just shoes made from fish scales; and they play with paper dolls cut from old magazines. Some things, however, continue as usual. Annemarie still plays with Ellen, and all of the children attend school. Annemarie's father and Ellen's father go to work the same as always.
Number the Stars begins with a foreboding tone. Annemarie, her sister, Kirsti, and Ellen are running home from school and are questioned by the Nazi soldiers. Mrs. Hirsch, the button store owner, and her son are taken away by the Nazis. When the Rosens, upstairs neighbors and good friends of the Johansens, go to their synagogue to celebrate the Jewish New Year, their rabbi warns them that they are in extreme danger of being taken and "relocated" by the Nazis. When the Johansens find out, they offer to help them because, "that's what friends do."
The Rosens must go into hiding or risk being relocated by the Nazis. Peter Neilsen, Lise's fiancé and a member of the Resistance, takes Ellen's parents with him on the eve of the Jewish New Year. Ellen stays with Annemarie and her family pretending to be Annemarie's sister. The tone is suspenseful as Nazi soldiers demand entrance to the Johansens' apartment in the middle of the night, searching for the Rosens. Terrified, Annemarie notices that Ellen has on her Star of David necklace. Annemarie yanks the necklace from Ellen's neck and hides it in her hand. Because Ellen has dark hair and Annemarie and Kirsti have blonde hair, the soldiers question Annemarie's father about Ellen's identity. He corroborates Ellen's story, telling the soldiers that she is Lise. Mr. Johansen produces a picture of his dead daughter, Lise, who had dark hair as an infant. The soldiers reluctantly accept the picture as proof and before they leave the apartment, they spitefully destroy the pictures.
The next day, Mrs. Johansen takes Annemarie, Kirsti, and Ellen to her brother's farmhouse which is in Gilleleje, near the coast. Annemarie knows the trip is not a vacation, but she doesn't understand what is going on. The night before, when her parents telephoned her uncle, they seemed to be talking in code. They talked about "good days for fishing" and transporting cigarettes. Although Annemarie knows her Uncle Henrik, is a fisherman, she doesn't know that he has been transporting Danish Jews to neutral Sweden by hiding them in a secret hollowed out area in the bottom of his boat.
The trip to Uncle Henrik's is extremely dangerous. On the train, the Nazis question Mrs. Johansen and when Kirsti starts to talk to the soldiers, they fear she will innocently reveal that Ellen is Jewish. At Uncle Henrik's, Annemarie is told that her Great-aunt Birte has died and that people are going to gather at the house to pay their final respects. Annemarie is confused because she doesn't have a Great-aunt Birte. A casket arrives at the farmhouse and soon after, strangers gather at the house and sit near the casket. Peter Neilsen arrives with Ellen's parents. Annemarie realizes that all of the people are Jews. Nazi soldiers arrive and question Annemarie about the contents of the casket. She bravely tells them that her Great-aunt Birte has died. She understands how dangerous the situation is and soon learns that her Uncle Henrik is going to smuggle the Jews across the sea to Sweden. The casket is full of blankets and warm clothing for the Jews to take on their journey.
The Jews make it safely to the boat; however, Mr. Rosen has dropped an important envelope that was from Peter to Uncle Henrik. The situation becomes complicated when Mrs. Johansen, who led half of the Jews to Uncle Henrik's boat, breaks her ankle on her way back to the farmhouse. The only person left to take the envelope to Uncle Henrik is Annemarie. Instructed by her mother, she puts the envelope in the bottom of a basket, puts food on top of it, and then rushes off to catch the boat before it leaves the dock. On her way to the boat, she has to take a path through the woods. She thinks about the story of "Little Red Riding Hood," in an attempt to maintain her courage. Annemarie encounters Nazi soldiers with dogs. She is scared, but remembers how her little sister, Kirsti, acted one day when Nazi soldiers stopped them. She acted impatient and angry. Determined to get the envelope to Uncle Henrik, Annemarie acts the same way. The soldiers let her go, and Annemarie makes it to the boat. She is able to give Uncle Henrik the envelope that contains a handkerchief. The handkerchief has a chemical on it that causes the Nazis' dogs to lose their sense of smell temporarily. After sniffing the handkerchief, the dogs are unable to smell Uncle Henrik's hidden "cargo" — the Jewish people who he is smuggling to safety.
The Rosens and the other Jews make it safely to Sweden. Two years later, when the war is over, Annemarie asks her father to repair Ellen's Star of David Necklace that she has kept hidden. She puts it on and intends to wear it herself until the Rosens return home and she can give it back to her friend, Ellen.