President Yoweri Museveni’s office has moved to explain why Uganda sent its troop to South Sudan even as pressure intensifies for their withdrawal.

Instability in South Sudan was likely to energise Joseph Kony’s Lord Resistance Army. There have been fears in Kampala about the re-emergence of rebellion following the falling out last year between President Museveni and former co-ordinator of intelligence services Gen. David Sejusa.

“Joseph Kony was a straggler after the defeat of Alice Lakwena and her Holy Spirit Movement. It was the revolt within the SPLA/M that linked up Kony firmly with Juba and Khartoum,” said David K. Mafabi, President Museveni’s private secretary.

Moreover, he said, President Museveni’s strong pan-African ideals and the need to safeguard his country’s economic interests underlie his decision to send troop to South Sudan.

South Sudan has emerged as the single biggest trading partner. Exports there are valued at $220 million per month, according to the Bank of Uganda. The two-month conflict partly explains the nearly $100 million shortfall Uganda Revenue Authority recorded in its half-year performance.

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With ever present threats of foreign aid being frozen, the government is trying to raise its own internal revenues. Last year, the Finance Ministry committed to financing 81.1 per cent of the national budget from internally generated revenues. Instability in its leading market, therefore, called for immediate intervention.

These factors remain in operation despite Kampala’s recent announcement of an imminent withdrawal of its soldiers from Juba. At the 4th Northern Corridor Integration Projects Summit that Kampala hosted on February 20, Dr Barnaba Marial Benjamin, South Sudan’s Minister for Foreign Affairs, paid glowing tribute to Uganda’s intervention and appeared to challenge other regional countries to emulate it.

“I would like to take this opportunity to thank foreign ministers of the Inter-Governmental Authority on Development (Igad) who responded positively and also to President Uhuru Kenyatta as well as Ethiopian Prime Minister Hailemariam Desalegn who actually flew in withing four days of the crisis. Where would they have found the confidence if Ugandan troops were not at Juba Airport? Would these countries have allowed their president and prime minister to fly into crossfire? It wouldn’t happen,” Dr Barnaba told the summit.

According to Simon Mulongo, a security expert, whereas the summit was officially about infrastructure development, President Museveni may have timed it to “seek a rethink by these countries about using their weight as the East African Community to influence events in Igad so that they do not disfavour Uganda’s interests.”

President Museveni and his close associates seem to have never got over Dr Riek Machar’s splintering of the Sudan People’s Liberation Army/Movement in 1991 and his subsequent alliance with Sudan’s President Omar al-Bashir.

This marriage gave Kony the lifeline upon which he founded the Lord’s Resistance Army and for the next 15 years wreaked havoc in north and parts of eastern Uganda. 

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“Khartoum, working together with Riek Machar, retrained, rearmed, and reorganised Kony first and foremost not to fight Uganda but to fight against the SPLA/M. Riek Machar has never severed his links with the LRA from that time up to today,” added Mr Mafabi, a onetime aide to the late Dr John Garang, the founding leader of the SPLA/M.

Dr Machar was, until July last year, President Salva Kiir’s deputy before he was sacked. He led the 2006 peace negotiations between the Ugandan government and Kony, who never turned up to sign the final agreement.