BAIDOA, SOMALIA, July 27 — In the past few days, phantom troops have reportedly flooded across the border from Ethiopia. Mysterious planes have landed in Mogadishu. Young gunmen in a kaleidoscope of camouflage are cruising the streets all over this country, their true allegiance one big question mark.

But in this land of secrets, one thing is clear: the two powers to reckon with in Somalia — the Islamic clerics who rule Mogadishu and the internationally-recognized transitional government confined to Baidoa — are headed on a collision course toward a full-scale war. And this time the crisis may spill far beyond Somalia’s borders.

Ethiopia and Eritrea, bitter enemies, are apparently already arming the two different sides and threatening to ignite ethnic and religious tensions across the Horn of Africa. Many people fear that if a major war breaks out in Somalia, Muslim tribes in Ethiopia’s deserts will rise up and challenge the Christian leadership; Islamists in Mogadishu will storm down the coast toward Kenya; Ethiopia and Eritrea will resume their costly battles; and countries like Sudan and Egypt, which have weighed in before, will weigh in again.

In anticipation of all this, Somalia’s transitional leaders are urging the United Nations to lift an arms embargo. They want more weapons to flow into a place already a free-for-all for armed groups, where an entire generation of young men has grown up with guns in their hands, not pencils.

Islamists in Mogadishu are calling for a holy war as they sweep across a victimized landscape desperate for order, gobbling up territory, absorbing militias and ultimately headed, many people fear, for Baidoa, the midsized town 150 miles away where the fledging transitional government is trying to take root.

The Baidoa government is rushing to fortify its buildings and unify its militias into a national army. But its leaders admit they are outgunned. And a little paranoid. And divided.

The Parliament meets in an old grain warehouse where politicians from different clans struggle to find consensus even with a common enemy, the Islamists, breathing down their necks.

In downtown Baidoa, donkeys snack on piles of garbage, children chant the Koran in bullet-pocked rooms that pass for schools and many people’s foreheads wrinkle up when they asked about their future.

The tensions spiked last week when hundreds of Ethiopian troops allegedly rushed into Baidoa to protect the transitional government. On Wednesday, a mysterious cargo jet landed in Mogadishu, and today there were reports of two more. The Baidoa government immediately accused Eritrea of shipping weapons to the Islamists, which the Eritrean government promptly denied.

United Nations diplomats are shuttling between Baidoa and Mogadishu, urging both sides to negotiate. Meanwhile, United Nations agencies are preparing for massive displacements of people that could result from a major conflict. The Baidoa government will return next week to the Sudan for another round of peace talks with the Islamists, hoping to strike an accord with moderate clerics but fearing it is the hardliners who hold the real power.

“It’s not our policy to fight,” said Ali Mohamed Gedi, the transitional government’s prime minister. “But the Islamists are expanding their muscles. It’s a very fragile time.”

In Mogadishu, the ruined capital, residents are stockpiling batteries, bottled water and other staples. At a rally this past week, thousands packed into a soccer stadium and chanted, “Death to Ethiopia.”

It’s a tale of two cities with no poetic ending in sight. Many people fear war in inevitable. The Islamic Courts Union, a grassroots uprising centered on strict Muslim law, is bent on creating an Islamic state, incompatible with the type of secular government the Baidoa politicians are trying to form. American officials claim some of the Islamist leaders are connected to Al Qaeda, and Washington tried to undermine the Islamists by supporting their warlord rivals, which only backfired.

The Islamists now control Somalia’s biggest city and have access to the country’s best ports and airfields and apparently a pipeline of weapons. But the Islamists can’t dismiss the Baidoa government, because it is recognized by western powers and backed up by Ethiopian muscle.

“Each side has a dream to get rid of the other,” explained Omar Faruk, a Somali journalist. “They’ll never share power.”

The truth about Somalia is that despite all the surface tensions between secularists and Islamists, it is clan allegiances that truly divide society. It’s been that way for centuries since clan-based tribes roamed the deserts and competed for grazing land. One reason why the Baidoa government is weak is because it was organized as a compromise between clans and is therefore riven by rivalries and mistrust. The political culture in Somalia has yet to catch up with the good intentions of the international experts who are trying to facilitate peace.

The Islamic Courts Union, on the other hand, is dominated by one clan, the Hawiye, and two of its larger sub-clans, the Haber-Gider and the Abgal. It is further united under the banner of Islam, though there was, at least initially, a leadership duel between the moderates and hardliners. That duel ended after word began to spread that Ethiopian troops were pouring into Baidoa and the masses rallied behind the most militant clerics.

Many people in Somalia, which is almost purely Muslim, view Ethiopia, a country with a deeply-rooted Christian identity, as a mortal threat. The two nations have feuded for centuries, most recently fighting a war in the late 1970’s.

“That was about the stupidest thing the president could do, inviting our archenemy onto our soil,” said Ahmed Mohammed Suleiman, a member of the transitional Parliament.

More than a dozen Baidoa politicians, including cabinet members, resigned in protest today, creating even more havoc. Some even defected to the Islamists, bringing with them their militia.

The chief of staff for the Baidoa government, Abdirizak Adam Hassan, said no one in Baidoa asked for Ethiopian troops and that Ethiopia had a long history of unilaterally crossing the 1,000-mile-long border to quash militant Islamists in Somalia.

“The reality is our government is weak,” Mr. Hassan said. “We can’t control our borders or our skies.”

United Nations officials provided detailed accounts of a middle-of-the-night arrival of hundreds of shock troops from Ethiopia, down to their polished boots. But the Ethiopian government denied any incursion, and during a three-day visit to Baidoa, this reporter did not see any identifiable Ethiopian soldiers, though his travel was restricted.

Ethiopian officials have said their forces would defend Baidoa if the Islamists attacked, and last week the Islamists came close. One theory now circulating is that this whole episode was a masterful chess move by the Islamists. They steamed up the road from Mogadishu in a convoy of battered pickup trucks with mounted machine guns and came within 25 miles of Baidoa, never intending to attack, the theory goes, but only to provoke an Ethiopian response, knowing full well the hysteria it would fuel.

United Nations officials have accused Eritrea of funneling arms to the Islamists as a way to antagonize Ethiopia. The two countries, once very close, recently fought a border war that cost tens of thousands of lives. Several Arab countries are also suspected of financing the Islamists.

Somalis find all this dizzying. They are used to their own clans fighting each other. Now they have to fathom their country getting torn apart by outsiders.

Hawa Eybeled, a Baidoa resident and businesswoman, who had 15 children but lost 8 to war and disease, is frightened about what lies ahead.

“What is it they say? When the elephants fight, the grass gets trampled.”