Shardik dramatizes complex problems concerning religion and family values. On a hunting trip, Kelderek of Ortelga encounters an immense bear. He realizes that it is the god Shardik, who has not been seen for many generations. Returning to Ortelga, Kelderek refuses to tell even High Baron Bel-ka-Trazet what he saw, claiming that he can inform only the Tuginda, the high priestess of Shardik’s cult. The furious baron nearly kills him but is interrupted by the startling request for a meeting with the Tuginda. They journey to the mysterious island of Quiso, where the Tuginda forms a party that includes the priestess Melathys in order to find the bear.
The Tuginda tells Kelderek the history of the Ortelgans, who once ruled the Beklan Empire and served Shardik. A corrupt priestess and her slave trader lover finally slew Shardik, and the empire fell. Centuries later, the priestesses wait for Shardik’s return. Another prophecy tells that God will reveal a great truth through Shardik and through two chosen "vessels," who will be "shattered" and refashioned to fit his purpose. The Tuginda believes that she and Kelderek are these vessels.
Kelderek finds Shardik, but Melathys is so frightened by the bear that she flees down the river. Under a young baron, Ta-Kominion, however, the Ortelgans rise and overthrow Bel-ka-Trazet, then follow the bear as it wanders to Bekla. Ta-Kominion tells Kelderek that they can reconquer Bekla if their attack is swift and if Shardik is with them—so Shardik must be drugged and brought there in a cage. The Tuginda protests that the Power of God must not be manipulated for greed and secular force, but Ta-Kominion shames Kelderek into helping him. When the Ortelgans encounter Beklan soldiers, Shardik awakens from his stupor, smashes out of the cage, and destroys the army. Within days, Kelderek becomes the priest-king of Bekla.
Five years later, the Ortelgans are at war with rebellious provinces led by General Erketlis; the Tuginda is imprisoned on Quiso; Shardik is behind bars in Bekla; and Kelderek unhappily prays to learn the mystery that Shardik is meant to reveal.
Elleroth, a southern nobleman, visits Bekla. Disliking the Ortelgans for their barbarous ways and their revival of the slave trade—and disbelieving in the godhood of Shardik—he sets fire to the royal house. Shardik gets free and escapes Bekla, and Kelderek follows to recapture him. After a horrific journey, he physically and mentally deteriorates, then falls into the hands of Elleroth’s army, where he learns how much he is hated for condoning the slave trade. Elleroth, however, allows Kelderek to go free—to Zeray, the lawless outland. There, he finds both the Tuginda and Melathys, and he learns that Bel-ka-Trazet, recently dead, had also come there and tried to create order. Kelderek realizes that he loves Melathys and decides to abandon his search for Shardik. They then learn that the bear-god is nearby.
Kelderek sets out again to find Shardik, this time to kill him, but he is captured by the evil slave trader Genshed. With the slave children, who include Elleroth’s son, he suffers horrendous tortures. Just as Genshed begins to murder the slaves in order to escape Elleroth’s approaching army, Shardik appears. Genshed shoots Shardik fatally with his bow, but the bear’s final blow likewise kills Genshed. Peace is restored, and Kelderek and Melathys, revealed as God’s vessels, civilize Zeray and adopt the slave children.