Beneath a Marble Sky is the story of a woman's journey to self-acceptance. Jahanara wants to love and be loved, according to the example her parents, Shah Jahan and Arjumand Mumtaz Mahal, have set, but in order to find love, even within the restricted world of a woman in seventeenth century Hindustan, she must first come to love herself. When her mother dies in childbirth, Jahanara tries to follow in her footsteps by advising her brother, Dara, and, at times, her father as well, but she never feels worthy of this responsibility. In the architect, Isa, she finds love and support, but in order to truly celebrate their love, she must first rid herself of the ties that bind, and her compulsion to prove herself worthy to her loved ones.

Thirteen-year old Jahanara, daughter of Emperor Shah Jahan and Arjumand Mumtaz Mahal, plays with her brothers and sisters in the harem of the Red Fort at Agra. She is a curious and clever girl, but she is conscious of the fact that she is close to turning the corner on womanhood. She loves her older brother, Dara, the heir to the throne, but her younger brother, Aurangzeb, frightens her with his jealousy and cruelty. At a river outing, Jahanara becomes convinced that Aurangzeb would have let her drown, and she begins to avoid him. Aside from Aurangzeb, her childhood is idyllic and privileged. She basks in the glory of her parents' love for each other and dreams of the day when such a love will be hers.

The perfection of Jahanara's childhood is shattered first by her arranged marriage, at age sixteen, to an older brute of a man, Khondamir, and then by the unexpected death of her mother in childbirth. The combined efforts of Jahanara, her father, and the court physician cannot save the Emperor's beloved wife. Before she dies, Arjumand makes Jahanara promise to watch over her father. Shah Jahan is heartbroken by her death, and he weeps in an agony of grief.

Arjumand's death leaves a huge hole in Jahanara's life, but she soon has a reason to overcome her sorrow. Shah Jahan calls on the greatest builder of the day, Ustad Isa, to construct an unparalleled mausoleum for his wife. The young architect is willing to take on the project, but requires a painting of Arjumand for inspiration. Shah Jahan offers the face of his daughter, Jahanara, as a mirror of her mother. The emperor also assigns Jahanara to the project to act as his agent when he is taken up with other matters of state. Jahanara finds love and acceptance with Isa, along with a stunned admiration of his vision for the great building that will honor her mother.

The mausoleum, which Shah Jahan names Taj Mahal using his nickname for Arjumand, develops slowly; the blocks of marble are heavy and awkward, and the foundation must be laid deeply to ensure its future stability. The work is difficult, but fulfilling. As the building grows, so does the love that Jahanara and Isa share. They are not free, however, to show their love in public. In her father, Jahanara finds a sympathetic heart. He makes secret arrangements twice for Isa and Jahanara to be together. They share their love in a safe house in the city that can be accessed by a long, secret tunnel from the Red Fort. Soon, they conceive a child. Jahanara has learned to manipulate her stupid, often absent husband, and she convinces him that the child is his. She safely delivers a daughter, whom she names Arjumand.

Meanwhile, her brother Aurangzeb fights for the Empire in Persia and the Deccan region, gaining physical strength and knowledge of war. His support among the nobles of the court increases along with his many victories. Dara, the heir, is the exact opposite. Philosophical and dreamy, he relies on his study of religious texts to guide his decision-making. He too has support among the nobles, but Jahanara fears that his gentle, tolerant disposition will be overrun by the ruthless ambition of Aurangzeb. Jahanara defends Dara when she can and keeps close tabs on Aurangzeb through her friend, Ladli, who becomes his lover in order to spy on him. Jahanara also sends Nizam, her faithful slave, off to fight in the army with Aurangzeb. She needs friends in these positions in order to defend her family against Aurangzeb's ambition.

Even though she sees the conflict between her brothers on the horizon, when she happens upon Aurangzeb late one night, transfixed by a cobra ready to strike, she cannot stand by and let her brother die. She slays the snake with Aurangzeb's sword. Aurangzeb then turns on her, accusing her of planting the serpent to assassinate him. His ingratitude angers her and she lashes out, making a permanent, powerful enemy of her brother. She has now chosen sides and cannot go back.

After eleven years, the Taj Mahal is complete, but with its completion, Shah Jahan loses his desire to live without his beloved Arjumand, and falls ill. Aurangzeb seizes the moment and makes a grab for the throne. Jahanara schemes desperately with her father and brother, Dara, to repulse Aurangzeb, but they are ultimately defeated in battle. Aurangzeb executes Dara and Dara's son for heresy, and then throws Jahanara and her father in a small cell that overlooks the Taj Mahal. Her only consolation is that Isa and their daughter, Arjumand, have fled the city and are safe from Aurangzeb's ruthless revenge.

Jahanara spends several years imprisoned with her father until her faithful servant, Nizam, comes with news of Isa, and a plan to escape. After bribing her jailers, she travels with Nizam to Bijapur, where Isa is being held prisoner as he builds a mosque for the Sultan. Jahanara strikes a bargain with the Sultan, offering the information that will help them assassinate Aurangzeb in exchange for Isa and Arjumand's freedom. The Sultan reluctantly agrees, but first Isa must complete the mosque.

After spending a week with her loved ones, Jahanara returns in disguise to Agra and her father, compelled to watch over him by her love and the promise she made to her mother. She finds him in a terrible state: weak, filthy, and near death. In her anger, she reveals her identity to the jailer who slams the cell door on her. Her mistake has put her right back in prison. She spends the time she has helping her father and making him comfortable again. Soon, however, her callous husband, Khondamir comes to wreak his own revenge for her faithlessness and insults. He rapes her brutally, but she manages to rally enough to curse him as he leaves her bruised and bleeding. Aurangzeb arrives at the cell to accuse her of again trying to assassinate him. He has his men torture her, wanting her to give up the name of her accomplice. Craftily, she names her lout of a husband. Aurangzeb kills him on the spot, but spares Jahanara in order to see her suffer.

Shortly after, Jahanara's father succumbs to his illness and dies. He is happy in his last moments to be joining his beloved in heaven. Aurangzeb stages an elaborate funeral at the Taj Mahal and demands that Jahanara be present and dressed in her best finery. He has her delivered to the harem, where the women clean her up and then scheme to help her escape. With the women's help, she breaks free of the Red Fort and finds Isa, Arjumand, and her friends, Ladli and Nizam, in Calcutta.

Together they make a life for themselves by the sea, finding the love of their small family preferable to the glory and danger of the Mughal court. They live on in peace into their old age, but after Isa's death, Jahanara decides the time is right to tell her granddaughters of their legacy. She does so in the shadow of the Taj Mahal, and as she does, she thinks about Isa, her beloved architect who built such a tangible testament to the power of love.