After newly installed DR Congo president Laurent Desire Kabila fell out with some of his countrymen, they formed rebel groups against him.
He had earlier fallen out with his two backers - Uganda and Rwanda, who had helped to install him in power after deposing Mobutu Sese Seko in 1997.
Mobutu, the self-styled 'King of Zaire', was president of DR Congo, which he renamed Zaire, from 1965 to 1997. He died in exile in Morocco.
Kisangani, the third largest city in DR Congo, became the theatre of war. The splitting of the rebel outfit Rally for Congolese Democracy (RCD) of Prof Wamba Dia Wamba into two, leading to a new outfit called RCD Goma and headed by Emile Illuga, in turn divided Uganda and Rwanda, who had hitherto been allies.
The Illunga faction was allied to Rwanda while the Dia Wamba faction was allied to Uganda, in effect forcing the Congolese factions to fight on either side.
On August 14, 1999, Uganda and Rwanda were engaged in the first military clash, largely sparked off by a fight for control of Bangoka Airport, one of the two airports in Kisangani. Both armies were based at the same airport, making it hard for any troop or equipment movement to go unnoticed since they were backing different factions.
The control of the airport was not only strategic militarily, but also economically strategic for both armies. Different international agencies would later point out that whereas there was no institutionalised plundering of DR Congo on the Ugandan side, the Rwandan side had what came to be branded as the 'Congo Desk' in the then vice president's office.
Night of the Kisangani clash
On the night of the Kisangani clash, the UPDF was commanded by the force's deputy commander in DR Congo, Maj Reuben Ikondere.
Maj Ikondere was to be killed by DR Congo footloose Mai-Mai militia fighters.
Then RPA's spokesperson, Maj Wilson Rutayisire, accused the Ugandan troops of triggering the attack.
While speaking to a French media outlet, Rutayisire said: "The fight is not about gold or diamond, but jealousies and divergence of strategy."
Just days after the clash, on August 10, 1999, Rwandan president Pasteur Bizimungu and his deputy and military strongman Paul Kagame met with President Museveni at the secluded Mweya Safari Lodge in Kasese to discuss the rising tension between the countries.
During the meeting at Mweya, modalities to normalise the operation of the two armies were agreed upon, including both armies withdrawal from Kisangani and having a neutral UN monitoring force in place.
With both forces out of the city centre for some time, in May 2000 Rwanda's defence spokesperson and presidential advisor, Maj Emmanuel Ndahiro, complained of troop movement on the side of Uganda, which he said was raising concern as it was not in the interest of the ceasefire agreed in Mweya.
On Friday, May 2000, the second clash erupted with the head of the UN monitoring team Lt Col Akram Hossian saying the Ugandan forces started the attack by pounding RPA positions.
A source that spoke on condition of anonymity for this story because he's still an active officer in the UPDF, says much as UPDF managed to defend their positions, a retaliation was inevitable against the RPA, who had caught them off guard.
After the second clash, Uganda's political Commissar James Wapakhabulo issued a statement in Kampala accusing the Rwandan forces of attacking the Ugandan positions. "The Rwandese fired at our positions at 4.05 in the morning. They fired at our training camp at Kapalata where we train Ugandan NCOs [Non-Commissioned Officers]. They fired at our positions from a bridge at Tchopo, 3.5 miles from Kisangani Town."
Tension continued to simmer between the two armies and their DR Congo rebel factions and it only remain a question of when another clash would be triggered.
Indeed, on Monday, May 8, in 2000, another clash, to be known as Kisangani III flared, with each side accusing the other of provocation.
This time round, Uganda's army commander Jeje Odongo said the RPA sprang the attack from bases at Lubuto junction and shelled Uganda's positions at Bangoka airport. The RPA spokesperson denied the accusations, but blamed the UPDF for triggering the attacks although he said they had trounced the UPDF.
On the other hand, Rwanda's government spokesperson Joseph Bideri said ORINFOR, the Rwandan national broadcaster, had showed some of the captured Uganda soldiers and military hardware from the UPDF. Though he didn't give number of how many fighters were captured, he said 18 Ugandan soldiers, including a captain and a lieutenant, had been killed, with no death or causalities on the Rwandan side. However, reports in Kampala indicated that 50 RPA soldiers had been killed.
Shortly after the third Kisangani clash, the Ugandan chief of staff and also commander of the Ugandan forces in DR Congo, Maj James Kazini, gave the RPA a 48-hour ultimatum to exit Kisangani or face their firepower.
But his Rwandan counterpart, Brig Gen Kayumba Nyawasa, dismissed the demands and countered that "RPA is not a battalion of the Uganda army to be ordered around on how and where to deploy."
This bickering could be traced to the time fighters of RPA left Uganda and invaded Rwanda in 1990.
Many of the RPA combatants were part of the rank and file and top brass of the UPDF.
This also implied their former rivalries, personal egos, and fights for supremacy with their UPDF counterparts had naturally been carried over into the new war theatre in DR Congo and set into play for the next two clashes as each side postured to prove their military prowess.
As a consequence, the two sides' crave to prove themselves over the other became an unavoidable contest of military prowess, sparking off the bloody Kisangani clashes in 1999, and 2000, with the ghost of war never completely buried.