Somalia’s long transition ended on August 20, with its war-battered capital Mogadishu more peaceful than it has been in 20 years.

However, the African Union peacekeeping mission, Amisom, which can claim credit for the change in Somalia, is not holding a victory parade yet.

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In often bitterly fought urban warfare, Amisom finally ejected the Somali hardline militant group Al Shabaab from all 16 districts of Mogadishu in May, bringing them under control of a central government for the first time in over two decades.

According to UN and Amisom figures, violence in Mogadishu has reduced sharply. Armed conflict plummeted nearly 70 per cent between April and June. Terrorist attacks were down nearly 50 per cent between May and June.

However for, especially, the East African countries that form the backbone of Amisom — Burundi, Kenya, and Uganda — and their Ethiopian allies, the gains and the defeat of Al Shabaab in central Somalia, have brought new headaches.

Diplomats tell The EastAfrican that the loss of several towns has forced Al Shabaab to dedicate its resources to defending the dwindling regions it controls in southern Somalia.

According to a UN Monitoring report, Al Shabaab has downgraded Mogadishu by placing it under the control of the group’s second deputy commander, while the rest of the leadership is concentrating on the south.

Ahmed Abdi Godane, its top leader, together with trusted lieutenants, are reported to be residing in the key southern port city of Kismayu.

Kismayu was the prize the Kenya Defence Forces (KDF) had in their sights when they entered Somalia last October.

Now “rehatted” as part of Amisom: other AU mission troops from Uganda, Burundi — and the Ethiopians — are all massing to launch an attack on Kismayu in a final battle against Al Shabaab.

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Analysts say that because Al Shabaab has been forced to take what will be its last stand in Kismayu, it could be “a fight to the death.”

By driving the militants out of lucrative locations and leaving them only with Kismayu, Amisom may have ensured that the fight for Kismayu will be a “Battle Royale,” as a commentator put it.

Amisom commanders, though, are unfazed. A commander in the Uganda contingent said that since the big battles for control of Mogadishu last year, Al Shabaab has mostly turned tail and ran when faced by a superior force.

He said they did not expect the militants to put up the kind of resistance observers think they will.

However, of great concern is what is happening in the north.

In his quarterly report on Somalia to the UN Security Council last week, Secretary-General Ban Ki-moon reported that Al Shabaab was undertaking frequent troop movements from southern and central Somalia to the semi-autonomous territories of Somaliland and Puntland, but noted that the insurgents’ focus on those areas was more on recruitment than terrorist activity.

Earlier though, a report by the UN Somalia and Eritrea Monitoring Group (SEMG) had painted a less benign picture.

SEMG reported that a group of fighters known as the “Galgala militia” in Puntland shifted allegiance to Al Shabaab early in the year.

This merger significantly boosted Al Shabaab’s presence in Puntland. Al Shabaab is also exploiting the deteriorating security situation in Puntland, and is assassinating governments officials and staging sporadic attacks on government facilities there.

In Somaliland, renewed military activities by the self-declared Khaatumo State led to clashes in various areas in June and July.

Though this encouraged Al Shabaab to go fishing in Somaliland for recruits, the growing instability could create fertile ground for the militants to set up shop.

The bright side of these developments, observers say, is that they make the unification of Somalia under a new democratic order more possible.

Meetings have been taking place between Somalia, Puntland and Somaliland leaders.

The irony is that while these territories peeled away because they were disgusted with the chaos of central and southern Somalia, they are more vulnerable today because they do not have a force the size of and with the superior weapons that Amisom has.

Somaliland and Puntland’s search for security under the Amisom umbrella could deliver the AU a bonus it never thought it would get when it waded into Somalia’s troubled political waters.

By the same token, Amisom officers say Somaliland and Puntland could give Al Shabaab a second chance, as they would reorganise more easily than they would in Amisom and Somalia government controlled areas. It is possible then that the Al Shabaab could open new fronts there.

One reason life for insurgents in central Somalia has become difficult, is the effectiveness of the Somalia National Security Agency (NSA), a security service that is little known outside Somalia.

It is the main intelligence arm of the soon-to-expire TFG.

The NSA has about 1,500 soldiers. It is led by the highly regarded Ahmed Faqi, and diplomats in the know say it has increased its capacity by recruiting many Shabaab defectors as informants.

It is credited with preventing several assassinations and terrorist bombings. The NSA has also been able to glean actionable intelligence from Al Shabaab operatives because of its newfound ability to eavesdrop on phone calls.

It’s the only TFG unit that receives superior training and a steady supply of money — believed to be mostly from the French and US.

An elite unit within the NSA, known as “Alpha Group,” is much respected, and is considered disciplined in ways other Somali forces are not.

Members of Alpha Group, a source in the know said, cover their faces all the time, and carry out the most daring operations in the capital. They are considered among the best such units in East Africa.

The fact that institutions like NSA have risen from the rubble of Somalia, gives the East African secretariat hope that a peaceful Somali can actually build the capacities to protect its newfound, albeit fragile, stability.

New worries

However, the success of the NSA, and the effectiveness of eavesdropping and covert operations, has one Nairobi-based consultant on Somalia (who asked not to be identified) very worried.

“You have these East African countries, Ethiopia, Uganda, Kenya, Burundi in Somalia, all countries that have passed laws or are trying to pass laws that would allow them to eavesdrop on mobile phone conversations and hack into emails,” he said.

“I gather they like what the NSA has achieved against Al Shabaab through things like eavesdropping, and my fear is that they will bring more of these methods home because Somalia has proved that they work,” he added.

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So it is not just East African government and armies that have new problems on their hands in Somalia, ordinary East Africans do too.

Somalia, it seems, is the region’s guinea pig for new security tactics that other governments are likely to apply.

Equally, East Africans went into Amisom totally green about warfare.

For example, Richard Rouget, a US security consultant, was quoted in Time Magazine as saying “The Ugandans [in Somalia] are one of the best urban-fighting armies in the world.”

It is a skill that will come in handy for the government anti-riot forces back home, as the country faces more and increasingly violent urban demonstrations in the capital and towns that are teeming with jobless and disaffected youth.

The NSA, however, might be the only bright spot as far as emerging Somalia security capabilities go.

Several assessments have reported that up to 50 per cent of police and military in Mogadishu are in the private employ of private individuals, businesses, and security firms, who often pay them double the government rate.

Rank and file soldiers are supposed to be paid $100 a month with officers receiving higher pay. But due to corruption and delayed funding, the salaries are paid late.

To put food on the table, many soldiers and police seek employment with the private sector, where they receive $200 — and, most importantly, on time.

In the records, the Somali government controls about 10,000 soldiers in and around Mogadishu. It is widely believed that up to 25 per cent of that are “ghost soldiers” who exist in name only and whose salary is collected and pocketed by different militia leaders.

Political leaders turn a blind eye, because the militia leaders are their allies. Of the remaining 7,500, it is estimated that nearly half are being paid by private individuals to protect them.

This privatisation of security is worrying, because of fears that in the post-transitional order, politicians and businesses who will be locked out of power, could rally around a new cause and organise armed revolt.

Already, confidential sources say there is evidence of some warlords arming themselves in anticipation of losing political clout.

Somalia, clearly, is still far from out of the woods. International response, therefore, seems to be anticipating a longer stay for Amisom.

Ki-moon, in his latest report to the UN Security Council, informed the world powers that the first phase of construction of permanent headquarters for Amisom, compliant with United Nations security standards, has been completed.

The UN would not be building a permanent office for Amisom if it thought the operation would be wound down in a year or two.

There are also fears that the international support for Amisom could spring its own problems. With Amisom now nearly at its full strength of 17,731, its budget has doubled to nearly $500 million a year.

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Though it has won a measure of public acceptance in Mogadishu, the disadvantage of the high cost of the mission is the resentment that it will attract from emerging Somali forces that are supported on a considerably smaller budget.

Donors are also reluctant to fund Somalia security forces because of their lack of credibility.

With the attack on Kismayu looming, attention is also beginning to focus on how a large measure of success in stabilising Somalia could affect relations between the region’s “Big Boys.”

Analysts say the most vexing division between the regional countries is not so much over who controls how much of the Amisom pie, but on differing approaches to Somalia’s future.

Because the “frontline states” (like Ethiopia and Kenya) share a border with Somalia, and confront a bigger problem with refugees and insecurity from Somali militants (kidnapping tourists and aid workers and sometimes killing them), they have their own proxies in Somalia.

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Ethiopia, for instance, backs Ahlu-Sunna Walijamaa and clan militias in central and southern regions of Somalia.

Kenya, to advance its objective of creating a friendly buffer zone in Jubba, too has its proxy militias, most notably Ras Kamboni. Everyone is watching to see how Djibouti will play its hand when its troops settle Hiran region.

On the other hand, Burundi and Uganda have largely been dispassionate about meddling in the local aspects of Somali politics.

This seeming even-handedness created a space in Mogadishu that has allowed many diverse Somali politicians to openly jockey for influence and power.

There are fears among some that these differences among the East African actors could put pressure on the level of harmony inside Amisom military operations. However, even the alleged even-handedness of Uganda is questionable.

Ugandan project?

Prime Minister Mohamed Abdullahi Farmajo was nudged to jump in June 2011 at the Somalia conference in Kampala, that wangled another year for the TFG.

His successor, the rather able Abdiweli Mohamed Ali, was seen as “project” of Uganda President Yoweri Museveni.

Early this week, reports on the BBC suggested that Kampala had threatened to withdraw its troops from Somalia if current Somali President Sheik Shariff were not elected. Kampala was quick to pour water on the reports.

Even after the transition, it seems Somalia will continue to be a story intertwined into the regional politics of the East African powers.