Abu Ali fled his life as a Shiite cleric and student in Homs, the besieged Syrian city at the center of an increasingly bloody uprising, but it was not the government he feared. It was the rebels, who he said killed three of his cousins in December and dumped a body in the family garbage bin. “I can’t be in Homs because I will get killed there,” he said from this religious city in Iraq where he has taken refuge. “Not just me, but all Shiites.” Like his fellow Shiites in Iraq, Abu Ali, who used his nickname to protect his family back in Syria, said he regards the Syrian rebels as terrorists, not freedom fighters, underscoring one of the complexities of a bloody civil conflict that has persisted as diplomatic efforts have failed. In spite of President Bashar al-Assad’s willingness to unleash a professional military on a civilian population, with lethal results, Mr. Assad retains some support at home and abroad from allies, including religious and ethnic minorities who for decades relied on the police state for protection from sectarian aggression. “What the government is doing is trying to protect the people,” Abu Ali said, echoing the Assad government’s propaganda. “They are targeting terrorist groups in the area.” The insurrection in Syria, led by the country’s Sunni majority in opposition to a government dominated by Alawites, an offshoot of Shiism, is increasingly unpredictable and dangerous because it is aggravating sectarian tensions beyond its borders in a region already shaken by religious and ethnic divisions. For many in the region, the fight in Syria is less about liberating a people under dictatorship than it is about power and self-interest. Syria is drawing in sectarian forces from its neighbors, and threatening to spill its conflict into a wider conflagration. There have already been sparks in neighboring Lebanon, where Sunnis and Alawites have skirmished. And here in Iraq, where Shiites are a majority, the events across the border have put the nation on edge while hardening a sectarian schism. As Abu Ali discovered, Iraq’s Shiites are now lined up on the side of a Baathist dictatorship in Syria, less than a decade after the American invasion of Iraq toppled the rule of Saddam Hussein and his own Baath Party, which for decades had repressed and brutalized the Shiites. “This is difficult,” said Sheik Ali Nujafi, the son of one of Najaf’s top clerics and his chief spokesman, of the Shiite support for Mr. Assad. “But what is worse is what would come next.” The paradox, of Shiites supporting a Baathist dictator next door, has laid bare a tenet of the old power structure that for so long helped preserve the Middle East’s strongmen. Minorities often remained loyal and pliant and in exchange were given room to carve out communities, even if they were more broadly discriminated against. As dictators have fallen in neighboring countries, religious and ethnic identities and alliances have only hardened, while notions of citizenship remain slow to take hold. The fighting in Syria has exacerbated that, as Shiites worry that a takeover of Syria by its Sunni majority would herald not only a new sectarian war but actually the apocalypse. People here say that is not hyperbole, but a perception based in faith. Some Shiites here see the burgeoning civil war in Syria as the ominous start to the fulfillment of a Shiite prophecy that presages the end of time. According to Shiite lore, Sufyani — a devil-like, apocryphal figure in Islam — gathers an army in Syria and after conquering that land turns his wrath on Iraq’s Shiites. “Among these stories we get from the Prophet and his family is that Sufyani will come out and will start to kill the believers in Syria, and then come to Iraq, where there will be many killings and massacres,” Mr. Nujafi said. He said events in Syria were “similar but not completely the same” as the story of Sufyani. With an easy grasp of history, he recalled the siege of Najaf and the sacking of Karbala, another holy city to the north, in the early 1800s by radically orthodox Sunni Muslims, an invasion that raised the same apocalyptic fears Shiites have now.