The Krishna Key centers around Professor Ravi Mohan Saini, the protagonist and a historian who has been accused of the murder of his childhood friend Anil Varshney, a famous archaeologist who has managed to decipher the script of Indus Valley seals.

In an attempt to clear his name, Saini looks into the past of Indian Mythology's grey and unexplored areas and uncovers the truth about a serial killer, Taarak Vakil who believes himself to be Kalki, the final avatar of Lord Vishnu.

Saini travels from the ancient ruins of the Lost City of Dvārakā to a temple in Vrindavan which was almost destroyed by the Mughal Emperor Aurangzeb in an attempt to discover one of Krishna's lost treasures, the Syamantaka gem, also known in alchemy as the philosopher's stone, and stop the killer from murdering his friends who are also under the threat.

Each part of the seal is in the possession of different people who are the descendants of the ancient Yadava tribe, namely Saini, Bhoja, Vrishni, Kukura and Chedi.

Sanghi stated that he "wanted to do a story in connection with the Mahabharata, but not retelling of the epic which has already been done" and undertook a month's research, saying that he "had to be extremely cautious in dealing with this topic as we put a premium on personal belief and faith".