The Secret of the Nagas is the second novel of the Shiva trilogy series by the Indian author Amish Tripathi. The story takes place in the imaginary land of Meluha and narrates how the inhabitants of that land are saved from their wars by a nomad named Shiva. It begins from where its predecessor, The Immortals Of Meluha, left off, with Shiva trying to save Sati from the invading Naga. Later Shiva takes his troop of soldiers and travels far east to the land of Branga, where he wishes to find a clue to reach the Naga people. Shiva also learns that Sati's first child is still alive, as well as her twin sister. His journey ultimately leads him to the Naga capital of Panchavati, where he finds a surprise waiting for him.
The story begins where The Immortals of Meluha ended. Shiva, the fabled savior of the land of Meluha, rushes to save his wife Sati from the Naga, the supposed killer of Shiva's friend Brahaspati. The Naga escapes, dropping a coin 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 in their journey by Shiva's General Parvateshwar, his associates Nandi and Veerbhadra, Ayurvati the doctor, and Bhagirath and Anandamayi, the prince and princess of Ayodhya. At Kashi, Parvateshwar gets mortally injured while trying to pacify a riot at the Branga community. Bhagirath is given a medicine by the Branga leader Divodas to administer on Parvateshwar. The medicine works and Parvateshwar is healed, but Shiva comes to know from Ayurvati that it contains herbs which is only available at Panchavati, the capital of the Nagas. He consults with Divodas and comes to know that Branga suffers from a plague, which has led them to ally with the Nagas, in return for benefits. Shiva decides to travel to Branga but Divodas informs him that to reach there special ships need to be made, which would take about six months.
As the ships are prepared Sati gives birth to Kartik. The journey to Branga starts, with Sati staying back at Kashi to help the King with a lion attack on the local villagers. When Sati and her soldiers are on the verge of losing against the lions, a group of Naga soldiers led by a man and a woman arrive and assist them in killing the lions. The Naga woman reveals herself to be Kali, Sati’s twin sister. She was denounced by their father Daksha since she was born with deformities, including two extra, functioning hands. The man reveals himself as Ganesh, Sati's first child, whom she believed to have died at child birth. Since Ganesh was also born with deformities which led to his face resembling that of an elephant’s, Daksha denounced him and lied to Sati. Both Kali and Ganesh are brought back to Kashi by Sati and they wait for Shiva’s arrival.
At Branga, Shiva learns that the only person aware of the medicine recipe is a bandit named Parashuram, who leads a secluded life and kills any man coming near his abode in the jungles. Shiva and his men defeat Parashuram, and to his surprise 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 leaves for Kashi with Shiva. At Kashi Shiva is introduced to Ganesh and Kali by Sati. Shiva recognizes Ganesh as the Naga who tried to attack on Sati and as the killer of Brahaspati. Severely angered, he leaves Sati and takes up residence at the Branga locality. One day, while playing with Kartik at a local park, three lions attack them and Ganesh becomes severely injured while saving Kartik. Shiva forgives him and together with Sat, 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, who disgusted with Daksha's deeds, asks him to leave Kashi and go back to Meluha.
Shiva decides to travel to Panchavati under the guidance of Kali, who is the Naga queen and knows the path through the Dandak Forest to the Naga capital. While traveling they are 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 she believes that the greatest secret of the Nagas lie. There in a classroom, Shiva finds Brahaspati, perfectly alive and teaching a class.