In 1939, Anne Frank (Hannah Taylor-Gordon) realizes her world is beginning to change around her. Eventually, the Nazis invade the Netherlands. Anne becomes increasingly distressed as her rights are taken away, and her family is ominously being forced to register as Jews with the government and to wear yellow stars. She is then forced to leave her school and attend a Jewish lyceum, where she meets her new best friend, Jacqueline van Maarsen (Victoria Anne Brown), who is only half-Jewish. Anne also meets Hello Silberberg (Nicky Cantor), on whom she develops a crush; it is implied that Hello also reciprocates her feelings. On her 13th birthday, she receives the famous checkered-patterned diary and immediately goes to her room to write her first entry.
A few weeks later, on a normal Sunday in July 1942, Margot (Jessica Manley), Anne's sister, receives a call-up from the Germans to be deported to a "labor camp" in the East. Otto Frank (Ben Kingsley) moves his family into the now-renowned "Secret Annex", followed soon by Hermann and Auguste van Pels (Joachim Krol and Brenda Blethyn), their son Peter (Nicholas Audsley), and Fritz Pfeffer (Jan Niklas), the Frank family's dentist. During their stay in the annex, the Van Pels family members are noted for their constant bickering. Fritz becomes Anne's antagonist, and Anne has her first serious relationship with Peter, from whom she receives her first kiss. All the while, she wishes for an end to the war. Anne also gets her first period while in the annex - an occasion that she had been anxiously awaiting. One night a thief breaks into the building below the annex, leaving the eight refugees in terror.
Eventually, on August 4, 1944, the Franks are denounced by Lena Hartog (Veronica Nowag-Jones), the cleaning lady of the business in which the annex resides. The eight people in the hiding are arrested and Anne's diary is dumped onto the floor while SS man Karl Silberbauer (Holger Daemgen) searches for hoarded money. Two of the helpers (of those in the Secret Annex) are also arrested. In conversation with Otto, Silberbauer is stunned to learn that he served as an officer in the Imperial German Army during World War I. Silberbauer laments that, if they had not gone into hiding, Otto and his family would have received decent treatment.
Afterwards, the Franks are sent on a train to Westerbork, a transit camp, where Anne, her family and friends are held in the criminal "S Barracks". There, Anne meets a woman, Janny Brandes-Brilleslijper (Klára Issová) and her sister Lientje (Zdeňka Volencová), who are later seen with Anne in Bergen-Belsen. Anne also befriends the camp's schoolteacher (Jaroslava Siktancova), who often invites Anne to the camp school to tell the students stories. (One of them is Mrs. Quackenbush, a story that Anne had written before going into hiding, and had been assigned to write by her math teacher as punishment for repeatedly talking in class)