In Ancient Egypt, Yocheved, a Hebrew slave, and her children, Miriam and Aaron, watch as Hebrew babies are taken and ruthlessly killed by Egyptian soldiers, as ordered by Seti I, a Pharaoh who fears an increase in the Hebrew population could lead to rebellion. To save her own newborn son, Yocheved places him in a basket and sets it afloat on the Nile, praying that God will deliver him to a safe fate. Miriam follows the basket and witnesses her baby brother being taken in by Queen Tuya, who names him Moses.

Twenty years later, Moses and his foster brother, Rameses, are lectured by their father after they destroy a temple during one of their youthful misadventures. Rameses is berated for their misdeeds though Moses tries to take the blame; Moses later remarks that Rameses wants the approval of his father more than anything, but lacks the opportunity. Seeking to give him this opportunity, Seti names Rameses Prince Regent and gives him authority over all of Egypt's temples. As a tribute to Rameses, the high priests Hotep and Huy offer him Tzipporah, a young Midian woman they kidnapped, as a concubine. After she nearly bites him, Rameses gives her to Moses, who he appointed Royal Chief Architect. That night he helps the Midian girl escape. While following her out of the city, Moses is reunited with Miriam and Aaron. Miriam tells Moses the truth about his past, despite Aaron's protests, and Moses denies it until Miriam starts to sing a lullaby that Yocheved sang for him the day she saved his life. That same evening, Moses has a nightmare that causes him to realize the truth. Moses asks Seti about the murder of the Hebrew babies; through his reply, Moses realizes that Seti considers the Hebrews inferior to him. The next day, Moses accidentally pushes an Egyptian guard off the scaffolding of the temple while trying to stop him from whipping a Hebrew slave, and the guard falls to his death. Ashamed and confused, Moses decides to go into hiding, despite Rameses' pleas that he stay.

Moses crosses many miles of desert, and eventually reaches the land of the Midianites, Tzipporah's people, who worship the Hebrew God. After Moses saves Tzipporah's sisters from bandits, he is welcomed warmly into the tribe by their father Jethro, the High Priest of Midian. After assimilating in this new culture, Moses becomes a shepherd and gradually earns Tzipporah's respect and love, culminating in their marriage. One day, while chasing a stray lamb, Moses discovers a burning bush through which God speaks to him. God instructs Moses to free the Hebrew slaves and take them to the promised land, and bestows Moses' shepherding staff with his power.

Moses then returns to Egypt with Tzipporah, entering the palace in the midst of a large celebration. He is happily greeted by Rameses, now Pharaoh and the father of a young prince. Moses tells Rameses to let the Hebrews go, demonstrating the power of God by changing his shepherding staff into an Egyptian cobra. Hotep and Huy boastfully "repeat" this transformation by using illusions to turn two staffs into two snakes, only to have their snakes eaten by Moses' snake. Having not believed his brother, Rameses takes Moses to the throne room where Moses discloses that he has honestly returned to free the Hebrews, and rather than being persuaded, Rameses is hardened and orders the Hebrew's workload to be doubled. Moses and Tzipporah go to live with Miriam, who forgives Moses for his former disbelief, and convinces Aaron and the other Hebrews to trust him. Later, Moses (with God's help) unleashes nine of the Plagues of Egypt (with the first one being copied by Hotep and Huy) to attack Egypt. As the days pass, the plagues ravage Egypt, its monuments, and people. Moses feels tortured to inflict such horrors on the innocent, and is heartbroken to see his former home in ruins. Despite all the pain and destruction caused by the plagues, Rameses refuses to relent, and in anger, when Moses confronts him again, vows to finish the work his father started against the Hebrews, unwittingly providing the stipulations of the final plague. Moses, with nothing left to say to Rameses, resigns himself to preparing the Hebrews for the tenth and final plague. He instructs them to paint lamb's blood above their doors for the coming night of Passover. That night, the final plague, the angel of death goes through the country, killing all the firstborn children of Egypt, including Rameses' own son, while sparing those of the Hebrews. The next day, Moses visits Rameses one last time, who finally gives him the permission to free the Hebrews and take them out of Egypt. Moses weeps at the sight of his dead nephew and for all his brother's pain.

The following morning, the Hebrews leave Egypt, led by Moses, Miriam, Aaron, and Tzipporah. They are weary at first, but soon begin to heal and find hope and happiness. They eventually find their way to the Red Sea, but as they are resting, they discover that Rameses has changed his mind and is closely pursuing them with his army. With only a few minutes separating the Hebrews from the Egyptians, Moses uses his staff to part the sea, while a pillar of fire blocks the army's way. The Hebrews cross on the open sea bottom; when the pillar of fire disappears and the army gives chase, the water closes over the Egyptian soldiers, and the Hebrews are safe. However, Rameses is spared, and he is hurled back to the shore by the collapsing waves, screaming Moses' name in anguish. Saddened by what he and Rameses have lost forever, Moses bids his brother goodbye one last time and leads the Hebrew people to Mount Sinai, where he receives the Ten Commandments from God.