"The Pearl That Broke Its Shell," tells the story of a young girl in present day, Rahima. As she goes through various hardships, her Khala (aunt) Shaima tells Rahima the story of her great-great-grandmother, whose story bears resemblance to Rahima's. In the novel, Rahima's story is told in the present day; Shekiba's story is told as it happened in the late 1890s and early 1900s. Since the girls' stories are told concurrently, in this study guide, both stories are discussed in the present tense.

Rahima is a young girl with four sisters, all of whom want to attend school but aren't allowed to as instructed by their father. As a semi-solution, Rahima's Khala Shaima, her mother's sister, recommends that Rahima become a bacha posh, or a girl dressed as a boy, so that she may attend school as well as run errands for the family.

As a bacha posh, Rahima feels free being able to wear pants and joke around with boys her age. She is only uncomfortable when she's approached by older men in the street when she is running errands. In fact, Abdul Khaliq is one of the men who has his eye on Rahima when she is a bacha posh. However, she stays a bacha posh longer than is traditionally accepted, thus angering her father, who is an opiate addict who barely pays attention to his family but is still easily shamed by any inappropriate behavior by his daughters and/or wife.

As a consequence for staying a bacha posh for too long and for disrespecting her mother, Rahima is married off to Abdul Khaliq, a warlord to whom Arif, Rahima's father, feels indebted. Part of the deal is for Rahima's two older sisters, Parwin and Shahla, to be married off as well to Abdul Khaliq's cousins. They are married off on the same day, much to the despair of their mother, other sisters, and Khala Shaima.

As Rahima, Parwin, and Shahla prepare for their nikkah, which is their wedding day, Khala Shaima tells the girls of their great-great grandmother Shekiba. She is a young girl about Rahima's age when Khala Shaima starts the story, which is thirteen years old. As a two-year-old, half of Shekiba's face melted when hot oil fell onto her face, thus deforming her for the rest of her life. Though Shekiba is accepted by her family, she is rejected and shamed by everyone else, strangers and extended family alike.

Shekiba loses her mother and siblings to a national wave of cholera, and then soon thereafter her father to extreme despair. Shekiba continues tending her family's land, eventually looking like a man due to the hard physical labor she does. Months after her father dies, Shekiba's extended family takes over Shekiba and the land, making her their servant. Eventually they give her as a gift to fulfill a debt, and she becomes another family's servant.

When Rahima begins her life as Abdul Khaliq's fourth wife, she faces jealousy from his other wives. Since she is new and young, Abdul Khaliq calls on her more often than the other wives. She is terrified, but she obeys his and his mother's every command, for fear of severe reprimands, though beatings become a regular part of her life.

Shekiba's story is told in between Rahima's story. She serves Azizullah's family for a time, but after she attempts to obtain the land left to her by her father, Azizullah and his wife Marjan don't trust her and work hard to get rid of her. They gift her to the king so he can use Shekiba as a bacha posh guard for his harem. The lead guard, Ghafoor, shows Shekiba around. Shekiba trusts and likes Ghafoor, but remains guarded so as to protect herself.

When Shekiba puts on her guard clothing, she feels awkward but free, since being in pants is completely different than being in a skirt. She is unsure of her situation, but is thankful for now that she seems to be out of harm's way. She is also thankful to be away from her grandmother, whom she cursed before she left her home.

Shahnaz is Rahima's house-mate. She shows Rahima around the house and tells her how the compound works and what to expect. She has no sympathy for Rahima and acts jealous toward her, however not as jealous as Badriya, Abdul Khaliq's first wife. On the compound, Rahima makes friends with Jameela, Abdul Khaliq's second wife. Jameela is the kindest wife and acts more like an ally than a competitor.

Rahima meets the other wives' children. Hashmat is Badriya's son, and he is about Rahima's age. When the two meet, they recognize each other from when Rahima was a bacha posh. She is embarrassed, and at the same time missing that time in her life. Rahima is treated as a servant for Badriya and her mother-in-law, who regularly treats her like an embarrassment to the compound.

Rahima bears a son, whom she names Jahangir. The fact that he is a boy keeps Abdul Khaliq's beatings to a minimum, however they are not absent. Rahima believes Abdul Khaliq cares special for Jahangir, since she sees Abdul Khaliq having special moments with Jahangir that he does not seem to have with his other sons.

Rahima is occasionally allowed to visit her sister Parwin, whom she notices seems unhappy. Khala Shaima is allowed to visit from time to time, which is how Rahima continues to hear Shekiba's story. The girls are not able to visit Shahla, since she lives much farther away. One day after Rahima thinks of visiting Parwin but puts it off due to her house duties, she finds out that Parwin has set herself on fire and died at the hospital.

As a guard, Shekiba does as she's told and fits herself into palace life. She does her job and doesn't complain, even when the women of the harem argue with each other and treat Shekiba rudely. Shekiba is given heavy tasks, as she is shown to have strength like a man from her days of working on her family's land. One evening when Shekiba is on night duty, she notices a man escaping from the concubine. She is unable to catch up with him to find out who it is, though she lets the other guards know so they might try. The man continues sneaking in and out of the concubine, but the guards never are able to catch him.

During one of her visits, Khala Shaima suggests to Rahima that she ask Badriya if Rahima may accompany Badriya to Kabul when Badriya goes to the parliament sessions. Rahima wonders to her Khala Shaima what would be the point, just like she wonders what the point was of the little education she received. Khala Shaima insists that Rahima's education will serve her well in the future, and tells her that Kabul would be a good experience. Rahima works up the courage to ask Badriya if she can accompany her under the guise of being her assistant, since Badriya can't read and Rahima can.

Jahangir is not allowed to accompany her to Kabul, so Jameela watches him. Rahima misses him greatly, but also enjoys her time in Kabul. She helps Badriya read, vote, and fill out documents. Rahima also attends a resource center meant for women of the parliament so they might improve their reading, writing, computer, and English skills.

Rahima continues drawing strength from Shekiba's story. Shekiba sees the King Habibullah's son, Amanullah, around the palace grounds from time to time. She thinks he's attractive, and she works out a plan to be the one he chooses for marriage, which is that she tells everyone with whom she interacts that she comes from a long line of women who bore mostly males so that he will choose her to be his wife. With Amanullah is Agha Aasif Baraan, one of Amanullah's trusted friends and advisors.

Shekiba's plan is ruined when one evening, Fatima, one of the women of the harem, falls ill. As the other women attempt to move Fatima into Benafsha's room, the girls discover that Benafsha has been having an affair when they see a man's hat lying haphazardly on the floor. Ghafoor goes to tell the king while the other women look after Fatima. Upon her return, she brings the news that the king has asked for Shekiba.

When Shekiba visits the king, she realizes that Ghafoor has blamed on Shekiba the entire situation of the mystery man, meaning that Shekiba is given the same punishment as Benafsha, which is imprisonment and then being stoned to death. Shekiba is angry; Benafsha is resigned.

During one of Rahima's visits to Kabul, Jahangir dies. She finds out from Jameela when she returns from Kabul that he fell ill soon after Rahima left for Kabul, but Bibi Gulalai, Rahima's mother-in-law, thought she could save Jahangir with tea and soup. Rahima is devastated and no longer sees purpose in her life with Abdul Khaliq. She is blamed for Jahangir's death by Bibi Gulalai and Abdul Khaliq, and therefore endures a harsher-than-usual beating from her husband as well as verbal reprimands from her mother-in-law.

Rahima mourns Jahangir long after the culturally-mandated 40 days of mourning are over. She returns to Kabul to assist Badriya at parliament. Unintentionally, Rahima shares her story with two women she met and has become friends with, Sufia and Hamida. The two women are members of parliament and are the ones who encouraged Rahima in the first place to attend the resource center. Sufia and Hamida escort a broken-hearted Rahima into the resource center, where they hope Ms. Franklin, the teacher, can help.

During imprisonment, Shekiba asks Benafsha why she had an affair. Benafsha insists Shekiba wouldn't understand, because it was for love. Shekiba overhears that her punishment may be changed, and in fact it is, as someone has requested Shekiba's hand in marriage. She hopes it's Amanullah, but knows it may not be. She must be present for Benafsha's stoning, though, and then afterwards she receives 100 lashings on her back as a replacement punishment for stoning. During her recovery, one of the other guards, Tariq, tells Shekiba that she is to be married in two days' time.

When Shekiba is brought forth for her nikkah, she learns it is Aasif Baraan, Amanullah's friend and advisor, who has requested Shekiba's hand in marriage. Shekiba knows Aasif was Benafsha's secret lover, and so it is as Aasif's wife she realizes that Aasif feels guilty, and since he couldn't save Benafsha he saves Shekiba. Another reason, brought to light by Aasif's first wife Gulnaz, is that Shekiba had bragged about being from a family that bore many sons. Since Gulnaz and Aasif have been married for a year at the point and Gulnaz has yet to produce a son, Shekiba is brought to the home as Aasif's second wife. Aasif is hoping that his shame will be erased by Shekiba bearing him a son, which she eventually does.

Though Shekiba deals with Gulnaz's aloof attitude much of the time, she is thankful to be living in a home where she is not beat and where there is only one other wife with which she must coexist. As she reflects on her life, she is glad to have taken the risks she's taken, since they have led her to a safe, sure life.

On her last visit to Kabul, Rahima pretends to fall ill so she can stay at the hotel room while Badriya attends parliament session. She is careful to be quiet as she puts on Hashmat's new clothing that she stole. When Rahima is certain that Hassan, the guard outside her room - but at the end of the hallway - is facing the other way, she opens the door as silently as possible, hoping he doesn't hear her.

Rahima makes her way out of her hotel room. She trips in the hallway, catching the attention of Hassan. He can only see the back of Rahima and so assumes it is a boy and does not go after her. Rahima makes her way out of the hotel, across town to where the proper bus will take her to a town far away. Though nervous she will be caught, Rahima finds the bus, gets off at the previously agreed-upon stop, and walks across the street to meet Ms. Franklin in a cafe.

Ms. Franklin has set up Rahima with a local woman's shelter, where she feels safe and secure away from Abdul Khaliq. Rahima writes to Khala Shaima, whose visits have been lessening in recent months due to Khala Shaima's ill health. Rahima writes of blue skies and singing birds, and she signs it, "Bibi Shekiba."