Apart from agreeing to push ahead with bilateral and tripartite infrastructure projects, Presidents Yoweri Museveni, Paul Kagame and Uhuru Kenyatta also struck a deal to fast-track plans for a political federation during their meeting in Kampala, which has been described as “a breakthrough.”

“I think it will be a breakthrough because we have been going round and round in circles,” Uganda’s Foreign Affairs Minister Sam Kutesa told The EastAfrican.

The three leaders agreed to fast-track plans for a political federation, alongside the more organic evolution of the Common Market into a monetary union, promising to put “accelerated energy into implementing it.”

They are expected to formally sell their position to their counterparts, Presidents Jakaya Kikwete of Tanzania and Pierre Nkurunziza of Burundi, who were not present at the Kampala meeting.

READ: Political unity talks to begin in November

Informal discussions were expected to take place as early as the last weekend of June during the Smart Partnership Dialogue in Dar es Salaam, which Presidents Kenyatta and Museveni were expected to attend.

The need to reaffirm the commitment to a political federation appears to have been prompted earlier this year when Tanzanian journalist Timothy Alvin Kahoho went to the East African Court of Justice and argued that the Heads of State Summit had violated the EAC Treaty in asking the Secretariat to draw up a roadmap to a political federation.

Although the court threw out the application, sources familiar with the matter say some of the actors keen on political federation saw this as an attempt to filibuster the process and sought to test support for the project among some of the principals.

The three presidents reaffirmed that support in a joint communiqué issued after the meeting and Mr Kutesa indicated in his comments to The EastAfrican that the deliberations were partly informed by regional events.

“We are reiterating some of the decisions that had been made, that the EAC Secretariat makes some kind of road map, especially now that the court has ruled on the recent case,” he said.

Officially, the meeting was not an EAC Summit and any decisions agreed upon that impact on the operations of the Community will have to be presented and formally discussed at the next Heads of State Summit in November. However, the three countries are free to pursue the more bilateral aspects of their agreements.

Officials in Kampala downplayed the absence of Tanzania and Burundi, pointing out that most of the deliberations were about infrastructure projects along the Northern Corridor.

But frustration with the slow turnaround of regional projects was evident in the words of one regional official.

READ: State of the EAC: Too many delays

“We have been talking of upgrading the railway for 10 years and nothing has been happening,” he told The EastAfrican. “We have to break the cycle of talking and talking.”

The agreements between the three leaders mean, at least in theory, that they will arrive in Arusha in November with a clear plan of action, which Tanzania and Burundi will have to either support or find grounds to oppose.

Such was the high-level nature of the discussion between the leaders that in one of the meetings only the principals were present, with President Museveni taking minutes, which they then presented to the junior members of their delegations.

The immediate outcome of the two-day Kampala talks was a declaration of executive authority to steam ahead with regional infrastructure projects and business reforms that have been crawling along for years.

For instance, the Eldoret-Kampala-Kigali oil pipeline extension project will now move ahead, more than five years after it was awarded to the Libyan firm Tamoil.

READ: Kenya, Uganda evaluate bids for fuel pipeline

Significantly, the three leaders agreed to work together to raise financing for an oil refinery in western Uganda, as well as a crude oil pipeline from Uganda to Lamu on the Kenyan cost, with a spur to South Sudan.

President Museveni has consistently advocated that the construction of the pipeline should be a regional project where all partner states become shareholders, rather than a Ugandan affair.

He reportedly revised the shareholding to propose a 40 per cent stake for Uganda, a 40 per cent stake for partner states and the balance for private investors including oil companies if they decide to participate. This is in sharp contrast to the 10 per cent stake that had been allocated to partner states in earlier documents.

READ: Challenges ahead for Uganda’s pipeline, refinery

According to information from the meeting, President Kenyatta agreed to engage with Uganda on the refinery rather than join the growing international lobby against it, arguing that Kenya’s refinery at Mombasa cannot meet current regional demand.

Kenya’s backing for an oil refinery in Uganda represents a win-win position for two reasons: The project continues to meet stiff opposition from the oil companies who prefer a crude export pipeline and Western interests that see multiple threats to the current status quo.

Agreement on a pipeline, seen as crucial to unlocking Uganda’s field oil development plans, and President Kenyatta’s commitment to expedite redevelopment of Mombasa port, locks the three countries into a large and strategic infrastructure network and raises questions about Tanzania’s participation as well as the plan for its proposed new port at Bagamoyo.

While many of the infrastructure projects are bilateral, such as the proposed joint construction of the Kapchorwa-Suam-Kitale road between Uganda and Kenya, it is the landmark agreement on the region-wide projects and policies in the absence of two member states, that is most revealing of the new core at the heart of the EAC.

For instance, the presidents said in a joint communiqué that they had discussed plans for a single Customs territory to collect taxes from ports like Mombasa in Kenya, Mpondwe in Uganda, Gisenyi in Rwanda, a common visa for tourists, and national identity cards, which Uganda currently does not have.

In what can only be considered a landmark ceding of sovereignty, each of the three presidents was given cross-border responsibilities: Kenya takes the lead on the pipeline and electricity generation and distribution; Rwanda on the Customs, single visa and EAC e-identity card; and Uganda the railway and political federation.

With review meetings scheduled in Nairobi in August and in Kigali in October, the three leaders could arrive in Arusha in November with tangible progress and in a strong negotiating position.

The new political realignment could affect not just the pace of the EAC’s move towards a political federation, but its geopolitical positioning as well.

“If you look at the map of East Africa, this deal creates an alliance of the willing from the Coast to Congo, and ropes in South Sudan too,” a source familiar with the matter told The EastAfrican. “The biggest question is whether Tanzania can quickly join the train and at what station.”

A wide-gauge railway line that extends all the way to Rwanda would also reduce the cost of transport on the Northern Corridor, securing Kenya’s position as the preferred import-export route, and relegating the Southern Corridor, through Tanzania to Burundi, to a distant, stand-by option.

The combo-projects also offers tangible political benefits for each of the three presidents.

President Museveni appears to have received renewed backing for his dream East African project, as well as participation in the kind of marquee regional infrastructure projects that are likely to enhance his legacy more than any project he can undertake at home.

A political federation in the EAC would be the crowning moment of a long military and political career and one that, as the only surviving member of both the Nyerere years and the revamp of the EAC back in 1999, he would see as a personal triumph and vindication.

Apart from reducing the cost of doing business in Rwanda, the long-term nature of such large infrastructure projects gives President Kagame a chance to cement and bolt down his country’s ties to the rest of the EAC and — should the people ask — a genuine reason to continue to serve in a public role after his scheduled retirement in 2017 when a few of the projects are expected to be complete.

READ: Now Rwanda’s transition hinges on amending law to keep Kagame

As for President Kenyatta, only large, regional-scale projects will allow him to eclipse the dramatic infrastructure projects undertaken by his predecessor, president Mwai Kibaki.

Apart from ensuring Kenya’s access to the vital markets of Uganda, South Sudan and the rest of Central Africa, the regional space allows him the warm welcome and accommodation that the rest of the world has been reluctant to offer in the aftermath of the International Criminal Court trial controversy.

President Museveni was gushing in praise for his Kenyan counterpart at a state dinner he threw for his guests at the end of the talks. All three will have been pleased with the outcome of their talks, but the feast in Kampala would have left some food for thought among a few other players in the EAC.

Analysts say the Entebbe proceedings indicated the first clear move to break away from the laborious consensus model of the EAC, to one where there is a “leading tendency” by a willing few.
Sources privy to the meeting’s organisation told The EastAfrican the absence of Presidents Kikwete and Nkurunziza was informed by sentiments that Tanzania, especially, seems more interested in the South African Development Community bloc, to which it also belongs, than it is in the EAC.

For Burundi, its capacity deficiencies have always meant the region would have to wait longer if it is to move in tandem with Bujumbura.

While President Kagame had initially been invited, his delay in joining his counterparts (he came in on Tuesday), the sources say, was informed by concerns that Tanzania especially could feel slighted at being left out.

The conspicuous absence of the other regional leaders including President Salva Kiir of South Sudan, potentially the next partner state of the Community — through whose country the pipeline transporting crude out of Uganda to Lamu port will pass — raised speculation as to the real intentions of this new alliance.

“Look, this was not an EAC summit; this was bilateral and there was no need to invite Salva Kiir because there is already agreement between South Sudan and Kenya on a pipeline project,” said Henry Okello Oryem, State Minister for Foreign Affairs.

There was also speculation in the region about what was drawing the trio together, with some suggesting that the decision to fast-track strategic infrastructure projects in the region masks an emerging regional alliance against the ICC spectre that hovers over the three leaders’ heads.

With President Kenyatta already an indictee over the post-election violence in Kenya in 2008, Presidents Museveni and Kagame are understood to be equally concerned about the possibility of summonses to the ICC over their militaries’ supposed activities domestically and in the region.

Sources told The EastAfrican that the trio is not insensitive to active attempts by “both state and non-state actors” alleging war crimes and crimes against humanity in which Museveni and Kagame are mentioned.

“How Uhuru’s case goes will form a template for the likely cases against them, thus the common interest,” he said, citing the Congo crisis in which the two leaders’ names keep coming up.

A development that builds onto this fear is that on his second African tour, US President Barack Obama has shunned all three of these countries, which are known to be strong allies of Washington in the fight against terrorism and Islamist regimes around the wider East African region.

READ: Why Obama chose Tanzania for his Africa tour

Besides this factor, Obama has family links in Kenya, but even before Mr Kenyatta won the presidential election in March this year, Washington had warned that an ICC-indicted president was a risk factor and a liability to relations between the two countries.

Clearly, by shunning the “allies” and opting to visit Tanzania besides Senegal and South Africa, Obama is sending a message that is not far removed from that of the ICC. However, government officials in Kampala argue that the three presidents are unfazed.

“ICC is a minor issue. Look, we are revolutionary sovereign states, and we cannot be colonised by the ICC. I can tell you Uganda will not accept being lectured by a development partner, or by any country or institution,” Mr Okello Oryem said.

But the ICC bogey for Museveni will not go away, especially following recent reports that an insider of his regime and top army officer General David Sejusa has taken his fight against the Ugandan leader to The Hague over war crimes and crimes against humanity that the army under Museveni as commander-in-chief, committed in the northern Uganda war between 1986 and 2006.

READ: Museveni’s dilemma as former ally fires salvo

The war has since been exported to Congo and the Central African Republic, where the Lord’s Resistance Army has found a safe haven.

Moreover, in its other military misadventures, the Uganda People’s Defence Forces has been accused of plundering the resources of neighbouring Congo, and committing crimes against humanity in the process as it fought wars ostensibly in pursuit of rebel groups such as the Allied Democratic Forces that waged war against the Kampala regime.

These war crimes and the argument that Museveni ought to face the ICC are amplified by former UN undersecretary for children in armed conflict Olara Otunnu.

“I have consistently said that all unexplained atrocities in northern Uganda that occurred after ICC came into operation (in 2002) are entirely under the ICC jurisdiction, and in every institution, accountability should be all encompassing,” he says.

Equally, President Kagame, whom reports of a UN panel of experts have accused of aiding and fomenting rebellion in eastern Congo as well as of perpetrating domestic human-rights violations documented in several Human Rights Watch reports, is a man not at ease.

Reported by Daniel Kalinaki, Gaaki Kigambo and Julius Barigaba