The arrival of Alexander the Great polarized the political loyalties of Samaritans and Jews, at least temporarily, because the Samaritans initially gave support to Alexander by contributing 8,000 Samaritan troops to his Egyptian campaign. While Alexander was in Egypt, the Samaritans revolted and killed the newly appointed governor,Andromachus. In retaliation, Alexander destroyed the city of Samaria and established a garrison of 600 troops there. Many of the Samaritans fled to ancient Shechem at the base of the mountain, and this became their chief religious center. The city they rebuilt at Shechem in 331 B.C.E. survived for more than 200 years, until it was destroyed by the Jewish king John Hyrcanus in 107 B.C.E.
By contrast, the Jews remained loyal to Persia and did not support the Greeks. In time, the Samaritans, sobered by Alexander’s destruction of Samaria and subsequent conflicts between Ptolemies, the Egyptian based branch of Alexander’s heirs and Seleucids, their Syrian rivals, shared Jewish wariness of the Greeks. However, the issue of Jerusalem versus Mt. Gerizim became a major factor separating Samaritans from Jews.
The latter site may or may not have included a temple. The rather limited documentary and archaeological evidence is ambiguous. The primary source is Josephus, whose stories related to the Samaritan temple suspiciously duplicate his own and other familiar stories of temple building. Samaritan sources seldom mention a temple or provide specific information about one. Archaeological remains are at best suggestive (see above); no local tradition corroborates it, and the Samaritan chronicles are vague. Their focus was the place rather than the structure, and the structure was likely quite modest.
Descriptions of Samaritan response to the reign of the Seleucid tyrant Antiochus IV (175–164 B.C.E.) are varied. 2 Macc 6:2 implies that the Samaritans unwillingly renamed their sanctuary after the Greek god Zeus Xenios. But Josephus claims they quite willingly renamed it Zeus Hellenios (Ant 12.257–64). The more resistant Jews were unhappy with the Samaritan position, as is evident in Jewish polemics of the time. The Book of Ben-Sirah connects the Samaritans with other secular enemies of Israel: the Edomites and the Philistines, and thus, the separation is completed: from a divergence regarding pure religious matters to ethnic enmity: “Two nations make my soul angry, and the third is no nation: The Edomites, The Philistines, and the foolish people that dwells in Shechem” (50:25-26).
Johanan Hyrcanus, Jewish governor and high priest, focused and expressed the deepest Jewish bitterness toward the Samaritans, and inspired by such anti-Samaritan stories as Genesis 34, which narrates the rape of Dina, Jacob’s daughter, by Shechem, the son of Hamor (recalled in The Book of Jubilees 30; Judith 9; and The Testament of Levi 5–7), destroyed the Samaritan sanctuary in 128 B.C.E. Shechem was also destroyed, and during the next decade most Samaritans drifted back to Samaria, leaving behind only a residual community at the foot of Gerizim but. In the Samaritans Sources , there is no reference, to that story of the destruction of the temple, neither to the existence of the temple on the summit of Mt.Gerizim. If there was such a story, which seared into the consciousness of the Samaritan people, it would necessarily be mentioned in the Samaritan literature in some way.