Number the Stars is set on a World War II timeline; the year is 1943 and the place is Copenhagen, Denmark. Although Germany has invaded the country, the Danish are stubbornly resistant to the anti-Semitic policies of the Nazi and quietly still follow the ideology of King Christian X. The narrative is seen from the point of view of ten-year-old Annemarie Johansen who lives in Copenhagen with her parents and younger sister Kirsti, who is five years old. She had an older sister named Lise who passed away from a hit-and-run case two years prior, only a few days before she was to be married. Annemarie’s best friend is a Jewish girl named Ellen Rosen. Although life has drastically changed for the Danish people in general since the German invasion three years ago, the Jewish community is seen to be suffering the most.
One day, while walking home from school, the three girls, Annemarie, her sister Kirsti and Ellen are intruded by two Nazi men who ask them a few questions. The girls are saved due to Kirsti’s rude behavior which fortunately the German soldiers find cute rather than insulting. The two older girls are shaken and retell the incident to their respective parents after arriving home. The mothers, Mrs. Johansen and Mrs. Rosen become frantic with worry and forbid the girls from conversing with the Nazis in any way.
A preview of life in German-invaded Denmark is given. Annemarie describes the lack of food and electricity in the streets, streets which are monitored by Nazis at all times of the day and night. People are in fear to risk an open rebellion although there is a Danish Resistance which is silently fighting back against Germany by helping Jews flee the country. A member of the Danish Resistance is Peter Neilsen who had been the fiancé of Annemarie’s older sister Lise. He regularly visits the Johansens although as Annemarie notices, since recently he has become busy with his work in the resistance.
Weeks pass by after the Nazi incident and one day, the three girls are sent to repair Kirsti’s button-torn jacket at Mrs. Hirsch’s store. When the girls arrive, they are surprised to see that the shop has been shut down due to the fact that Mrs. Hirsch is Jewish. After hearing this news, Mrs. Johansen becomes even more worried and that same night, Peter visits their home. Annemarie is brought into the living room while the adults talk and readers can catch from the conversation the adults have with her that they are all in one way or other actively assisting the Jewish by keeping them safe. At one time, Peter remarks that things are only going to get even harder for the Danish Jews from now on.
Soon, the Jewish New Year is upon them all, an event Ellen is very excited about. She speaks of the plans she has made about the celebrations but on that day, Mrs. Johansen reveals to the children that the Rosens are going away for a while and that Ellen is to stay with Annemarie and her family for the time being. Mr. Johansen further explains the situation by stating that the Germans are beginning to round up the Jews and send them to prisons so the Rosens have to go away with Peter into safety. They cannot take Ellen with them for the time being who will have to pretend to be a Johansen.
The Rosens go away and the same night, the Nazis come looking for them to the Johansens’ place. Although the family denies having any knowledge about their whereabouts, the German police are suspicious and decide to search the house anyway. They question Ellen’s identity since she has dark hair while the Johansens are all blond. However, Mr. Johansen shows the Gestapo a picture of young Lise who had dark hair too to pass off Ellen as Lise, his daughter.
Shaken by the previous night’s incident, Mrs. Johansen keeps the girls from school the next morning. Instead, she takes them to visit her brother, Henrik who lives in Gilleleje, a village near the sea that joins Denmark and neutral Sweden. They take a train ride to their destination and are once again apprehended by a few German soldiers who attempt to manipulate Mrs. Johansen into admitting that she is Jewish by asking her if she plans on celebrating the Jewish New Year. She sees through the ploy and says no, although Kirsti nearly gives Ellen away by revealing her Jewish ethnicity although she realizes her error at the last second.
They reach the village and the girls enjoy a beautiful day basking under the beauty of Gilleleje. Annemarie promises Ellen that she has kept her Star of David necklace safely, an ornament Annemarie had ripped from her friend’s neck the night before. The next day, Henrik reveals to the family that his great-aunt Birte has passed away and that a wake shall be arranged for them to mourn her. Since Annemarie is aware of the fact that there is no great aunt Birte in their family, she confronts her uncle about his apparent lie. Uncle Henrik asks Annemarie to go along with the lie since it is easier to be brave if you do not have all the facts. Later on, young Annemarie realizes what her uncle meant by these words.
A wake is arranged for Aunty Birte and a small number of guests arrive to attend the event, along with Mr. and Mrs. Rosen accompanied by Peter Neilson. Alarmed by the number of people in one residence, soon the German soldiers arrive in order to investigate the matter. Mrs. Johansen shows the soldiers the casket and explains that they are mourning a death. The soldiers are perplexed since it is not in the Danish custom to arrange to mourn with the casket closed. They demand to see the remains of the dead body but quickly retreat after they are told that the deceased had died of typhus and her body may still contain some of the disease’s bacteria. The Germans leave afterward although just to be assured of free of suspicion, Peter reads aloud a psalm. Eventually, the casket is opened, revealed to contain warm clothes for the guests who are in reality all Danish Jews attempting to flee from the country.
Mrs. Johansen and Peter take the Jews in small numbers near the sea where they will travel by Henrik’s boat all across to Sweden. Now aware of the real operation, Annemarie is unable to sleep all night and waits in apprehension for her mother. At the crack of dawn, she suddenly wakes up and finds her mother lying in pain near a way into the woods. She explains that she had tripped on her way back home after delivering the last of the refugees to the boat but dared not cry out for help in fear of giving away the operation. Annemarie helps her mother up and into the house and on the way, she finds a packet on the ground. It was supposed to be given to Uncle Henrik; without the packet, the operation is doomed to fail. Mrs. Johansen instructs Annemarie to hide the packet in a picnic basket and deliver the basket to Uncle Henrik before they have to leave for Sweden.
Annemarie keeps her head down and prays that no German sees her on the way. She repeatedly narrates the story of the Red Riding Hood to herself in order to distract her from the possibility that the ending of her story may not be as happy as the fable’s. She finally reaches the harbor and only then does she get caught by a bunch of German soldiers and their dogs. They search her lunch basket and find the packet, which when opened is shown to contain only a handkerchief. The dogs sniff the packet but there is no evidence of any funny business. So the Nazis let Annemarie go who safely delivers the basket to her uncle. Later on, Henrik reveals to Annemarie that the packet contained a special type of drugs that rendered the dogs incapable of finding the smell of the Jews hidden in a hidden section of the boat. She thanks Annemarie for her pivotal part in helping the Jewish people safely escape.
The timeline shifts up two years to show that the war is over and Denmark is finally free from the torments of the German soldiers. The finality of the characters is shown. Peter Nielson had been caught by the Nazis and executed for being a member of the Danish Resistance. Annemarie also learns that her sister Lise was also a member of the resistance and that her death was not an accident, rather it was engineered by the Nazis for her active role in rebelling against the German invasion. Now that war has ended, Annemarie awaits the return of the Rosens although there is no concrete evidence that they have survived after all. Nevertheless, Annemarie keeps Ellen’s necklace safe as she had promised.