Summary of the book - The Secret of the Nagas by Amish Thripathi

Continuing from The Immortals of Meluha, Shiva, the fabled savior of the land of Meluha, rushes to save his wife Sati from a Naga who escapes, leaving behind coins with strange engravings. After consulting with Sati's father Daksha and Dilipa, the king of Ayodhya, they come to know that the coin belongs to King Chandraketu, the ruler of the land of Branga in Eastern India. Shiva and Sati travel to Kashi, where a community of Brangas inhabit, in order to get more information on the Nagas. They are accompanied by Shiva's general Parvateshwar, associates Nandi and Veerbhadra, Ayurvati the doctor, and Bhagirath and Anandamayi, the prince and princess of Ayodhya. At Kashi, Parvateshwar is mortally injured in a riot at the Branga community. Their leader Divodas gives Parvateshwar a healing herb which works. Shiva learns from Ayurvati that the herb is only available at Panchavati, the capital of the Nagas. Divodas explains that they get the herbs from the Nagas due to a plague infesting Branga. Shiva decides to travel to Branga and Divodas orders special ships to be made for the journey.

Meanwhile, Sati gives birth to Kartik, her son with Shiva. As he leaves for Branga, Sati stays back at Kashi to prevent a lion attack on the local villagers. They are helped by a group of Naga soldiers, led by a man and a woman, who assist them in killing the lions. The Naga woman reveals herself to be Kali, Sati's twin sister and the man as Ganesh, Sati's child from her first marriage believed to have died at birth. Both were denounced by Daksha since born with deformities. Kali had two extra functioning hands while Ganesh's face resembled that of an elephant's. An overwhelmed Sati brings back Kali and Ganesh to Kashi.

At Branga, Shiva meets the recluse bandit Parashuram, who can enlighten him about the Nagas and the medicine. After defeating Parashuram, Shiva comes to know that he is a Vasudev, the group of scholars who have been guiding him on his journey. Parashuram is also surprised to see Shiva as the fabled Neelkanth; in remorse for his actions, he severs his left hand. He gives the recipe of the medicine to the people of Branga and joins Shiva's entourage. At Kashi Shiva is introduced to Ganesh and Kali by Sati. Shiva recognizes Ganesh as the Naga who attacked Sati and as the supposed killer of his friend, the scientist Brahaspati. Enraged, he leaves Sati and takes up residence at the Branga locality. One day, while playing with Kartik at a local park, Ganesh saves them from a lion attack. Shiva forgives him and together with Sati, confronts Daksha, who confesses to murdering Sati's first husband and denouncing Kali and Ganesh. Daksha blames Shiva for causing distrust between him and Sati; he is asked to leave for Meluha.

Shiva travels to Panchavati under the guidance of Kali, who is the Naga queen and knows how to reach the capital through the treacherous Dandak Forest. On their journey, the entourage is attacked from the river side by a cache of ships containing the weapons of mass destruction known as Daivi Astra that was once forbidden by Lord Rudra, the legendary supreme ruler of India. After fleeing from the attack and safely reaching Panchavati, Shiva and Sati suspect Daksha to be behind this. Kali takes Shiva to a nearby school in the capital, where he finds Brahaspati, perfectly alive and teaching a class.