Baal was born in the highlands of Canaan, a storm god whose name simply meant "Lord" in the Semitic languages of the Levant. In his homeland he was the son of El, the high god of the Canaanite pantheon, and the brother and consort of Anat, the warrior goddess who waded through pools of blood and ground the bones of her enemies. His myth was recorded in the Baal Cycle, a series of clay tablets found at Ugarit on the Phoenician coast, which told how he defeated Yam, the god of the sea, and later died at the hands of Mot, the god of death, only to be resurrected by Anat's fury. By the time Egypt's New Kingdom pharaohs pushed their empire into Canaan and Syria, Baal was already the most popular god of the region, and the Egyptians did what they always did with powerful foreign deities: they adopted him.

The syncretism between Baal and Seth was natural and profound. Seth was the Egyptian god of chaos, storms, and the desert, the red-haired outsider who had murdered his brother Osiris and fought his nephew Horus for the throne of Egypt. Baal was the Canaanite god of storms and war, the outsider who ruled the foreign lands beyond the Sinai. Both were associated with the desert wind, the thunderstorm, and the serpent. The Egyptians began writing Baal's name with the Seth animal determinative, the mythical creature with the curved snout and forked tail that represented Seth in hieroglyphs. On the so-called Stela of Year 400, a monument erected during the reign of Ramesses II, Seth is depicted with a human face and Levantine garments rather than his traditional Egyptian form, looking more like Baal than himself. The identification was so complete that the two gods became interchangeable in Egyptian texts: Seth-Baal, a single deity who combined the chaos of Egypt with the storm-power of Canaan.

The defining Egyptian myth of Baal survives in the Astarte Papyrus, a fragmentary text from the Nineteenth Dynasty that tells the story of his combat with Yam, the personified Sea. In the Egyptian version, the Ennead, the council of nine gods who shaped the cosmos, grows afraid when Yam threatens to flood the earth and demands tribute. The god Ptah, the craftsman creator of Memphis, and the harvest goddess Renenutet appeal to Astarte, the Canaanite goddess of love and war who was viewed as Ptah's daughter in Egypt, hoping she will act as a tribute bearer. Astarte, described as a fearsome warrior, strips down and brings offerings to the sea, a humiliating mission for a goddess of battle. Eventually Seth arrives, now fully identified with Baal, and fights Yam. The rest of the papyrus is too damaged to read, but the Hearst Medical Papyrus confirms the outcome: it implores Seth to expel illness from the patient "just like he vanquished the personified Sea." The myth had crossed from Canaan to Egypt and become part of the healing magic of the Nile valley.

Baal's worship in Egypt was institutional and official. His cult appeared in the Eighteenth Dynasty, around 1550 BCE, complete with a temple and priesthood at Memphis, the ancient capital that sat at the apex of the Nile Delta. The temple was called Per-Baal, the House of Baal, and it stood alongside the shrines of Egypt's native gods as a testament to the kingdom's imperial reach. During the Nineteenth Dynasty, under Ramesses II, the cult moved to Pi-Ramses, the great Delta city the pharaoh built as his capital, where Syrian and Canaanite populations had settled in large numbers. Ramesses II was particularly devoted to Baal and his circle: he adopted Anat as his personal guardian in battle, named his daughter Bint-Anat, "Daughter of Anat," and called his war hound "Anat in vigour." In the inscriptions of the Battle of Kadesh, the greatest military confrontation of his reign, Ramesses II is described as "Seth, great of strength, and Baal himself," a pharaoh who claimed the storm god's power as his own.

Baal was depicted in Egyptian art as a powerful warrior with a curved Syrian-style beard, a horned helmet, and a variety of weapons: a sword, a club made from a cedar tree, or a thunderbolt. He stood in the Levantine manner, legs apart, ready for combat, rather than in the rigid Egyptian pose. His consorts in Egypt were Anat and Astarte, both Canaanite goddesses who had been adopted into the Egyptian pantheon alongside him. Anat was the warrior virgin who avenged Baal's death by cleaving Mot with her sword, grinding his bones, and feeding them to the birds. Astarte was the goddess who stood on a lion and held flowers, a deity of both love and battle. Together they formed a triad of foreign power that the Egyptians respected even as they kept it at the margins of their native religion.

The cult of Baal in Egypt faded with the New Kingdom. As Egypt withdrew from its empire in Canaan and Syria, the need for a Canaanite storm god diminished. The Twentieth Dynasty saw the last major attestations of his worship, and by the Third Intermediate Period he had become a memory, condemned in the Hebrew Bible as a false god and a rival to Yahweh. Yet his identification with Seth survived in unexpected ways. The Greeks, who encountered Seth through Egyptian sources already filtered through foreign syncretism, called him Typhon, a name that carried echoes of Baal's storm-demon character. And the biblical condemnation of Baal worship, recorded in Jeremiah and the books of Kings, preserved his name long after the last Egyptian priest had forgotten the rites of Per-Baal.