"Pesantren" offers rare access inside an Islamic boarding school, and an insight into a traditional educational system that fosters good character-building based on a peaceful religious teaching that has been practiced in Indonesia for centuries. Raising their students to respect and to have compassion towards others despite their differences, these schools are Indonesia's last defense in the face of today's rising extremism.

Erni realizes there is something off with her "boarding school" daughter after reading the grocery list.

Ten girls get a mysterious invitation to stay in a dream boarding school. The secluded school was built by Gus Budiman to provide a second chance for those who have a dark past. Sissy, a model, came with her friend, Inong, who keeps their own problems. Butet has drugs problem. Sri comes with a prostitution scandal. While Rini who is looked innocent, gets pregnant out of wedlock. There are also other names with their own problems. Including Eni, a young policewoman, intelligent and ambitious, who is investigating the murder case at the Crystal Hotel and gets clues that the suspects are in the dream school.

Shila (Yuki Kato), daughter of a fisherman around Lake Toba, wants to go to favorite high school in Medan. But alas, Mother wants her to enter into the pesantren (religious boarding school). Shila complains to Father. This time Father agrees with Mother. Shila disappoints and their relationship is strained. Pesantren’s life is full of activities and disciplined, making Shila difficult to adapt. She becomes homesick. Even so Shila still dreams of being a novelist. Together with his friends, Manda (Febby Blink), Ayesha (Via Blink) and Icut (Vebby Palwinta), she discovers the meaning of true friendship. They even have a "pot of tears", where they keep all of sad and happy tears. Shila’s life at pesantren is decorated with colorful typical problems of adolescence.

Aso who has a passion for watching football at the stadium every time his favorite team competes, is put into a pesantren (Islamic boarding school) by his parents. The condition of the pesantren causes Aso to no longer be able to freely channel his hobby of watching it to the stadium. Aso then becomes friends with Dul, Yos and Sultan, who came from different regions. pesantren then make their friendship exceed the closeness with their own siblings. They then establish friendships as "biological friends".