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Tensions had been quietly simmering between Uganda and Rwanda long before the end of the deadly second Congo war in which the armies of the two neighbouring countries’ armies clashed.
The turf for the clash of the two erstwhile firmest of allies was in Kisangani, the capital of Tshopo Province in the Democratic Republic of the Congo (DRC) in August, 1999.
At least 1,000 people, mainly Congolese, are believed to have perished in the clashes between the two alone.

The two countries had backed rebels to oust former DRC president Laurent Kabila, who they had helped topple long-serving dictator Mobutu Sese Seko, but their disagreements had ended in on and off clashes for months in Kisangani. The clashes in Kisangani were soon ended, but as The Monitor, now Daily Monitor, would bring it to light, only the battle, not the war was over.
On October 14, 2001, The Monitor, quoting “impeccable sources”, ran a cover story entitled “Rwanda prepares for war – Uganda”, which suggested fears within the Ugandan military and security establishments. This, we reported, had forced Ugandan authorities to request the British government to increase the military expenditure in order to counter the suspected aggression from her neighbour.

The Sunday Monitor story did not directly state, as it would later emerge, that President Museveni had personally written to the British Overseas Development Minister then, Clare Short, seeking to, among other things, raise the defence expenditure beyond the 1.9 per cent of GDP to which it had then been capped in agreements with donors.
Mr Museveni needed the UK government support to increase the defence budget from US$133 to US$ 252m over the ensuing three years.

Faced with a threat from her neighbour to the south west, it was believed, and as The Monitor would report, the Uganda government wanted to bolster its position with the defence spending in case of war.
Sunday Monitor, quoting military sources, also revealed that there were fears within Uganda’s military establishment that Rwandan undercover agents and Ugandan dissidents had been recruited and were undergoing training in Rwanda and DRC to overthrow the government in Kampala.
In the letter, later confirmed to have been issued by him, President Museveni described his Rwandan counterpart as “ideologically bankrupt”.

Rwanda, through spokesperson Joseph Bideri, dismissed Uganda’s claims and fears as “disgraceful and primitive”. In case things went from bad to worse, Mr Museveni was also reported to be building an international coalition to back Uganda’s position.
In reporting the story, Mr Andrew Mwenda relied on sources both in the United Kingdom and Rwanda. It would later emerge that the Rwandan government had circulated Mr Museveni’s August 28, 2001 letter to Ms Short to leaders in the Great Lakes region, key diplomats at the UN headquarters in New York, and media after the possibility of war became imminent.
Ahead of the 2001 presidential polls in which Dr Kizza Besigye first challenged President Museveni, Uganda declared Rwanda a “hostile state”, a move that was backed by Mr Museveni in a letter forwarded to Parliament by the President’s Office. Rwanda, the authorities in Kampala believed, had funded and backed Dr Besigye’s candidature.

The subsequent defection of Lt Colonel Samson Mande, a former Uganda military attaché to Tanzania, together with UPDF Lt Colonel Anthony Kyakabale to Rwanda did not help the situation. The duo declared they would wage a “democratic struggle” against the Museveni-led government. Col Mande would also publish a letter accusing Mr Museveni of having betrayed Uganda’s liberation objectives.
From the Rwandan side Maj Alphonse Furuma, together with several other army personnel and youth, had fled to Uganda. Maj Furuma issued a letter critical of the Kigali government, accusing President Kagame and the ruling Rwandan Patriotic Front (RPF) of “criminal management” since coming to power in July 1994.
As attempts were later being made to repair Uganda’s relationship with Rwanda, Col Mande in a telephone interview with The Monitor, would dismiss allegations of waging an armed struggle against Uganda, but maintained he was involved in a struggle to return democracy in the country.

On either side of the Ugandan and Rwandan border, movements of troops were reported by April 2001. The Monitor would, in an October 25, 2001 cover story entitled “UPDF-RPA amass at border, pressure grows to avert war”, break the news of similar developments. Attempts to downplay the tensions through meetings of both leaders had not yielded much. The clock was ticking.
On the same day, Sunday Monitor broke the news of a looming war between the two countries, this newspaper also reported the story of the arrest of 10 Rwandan nationals by an anti-terrorism task force on suspicion they had entered Uganda to commit terrorism-related crimes.

Rwanda described the move as an attempt to frame her citizens and to portray the country as a state-sponsor of terrorism machine. A month before the incident, the terrorist group al-Qaeda had launched a series of four coordinated attacks on US soil that left more than three people dead. Being accused of terrorism was perhaps the worst label anybody have, individual or state.
Reacting to the Sunday Monitor story two days later, then Defence Minister Amama Mbabazi acknowledged that Uganda and Rwanda were not the best of friends at the time. He, however, downplayed the possibility of war between the two.
“I pray that it does not occur to anybody’s head that Uganda and Rwanda should engage in a military confrontation because it can be costly,” he said.

In the same story, this newspaper confirms access to documents that detail Uganda’s fears about Rwanda at the time, which it withheld following pleas of “national security” from the authorities.
Speaking on Andrew Mwenda Live, then aired on Monitor FM which morphed into KFM, Gen David Tinyefuza, now David Sejusa, defended President Museveni’s statements in the letter to Ms Short, arguing that the threat the President was talking about could have been circumstantial.
At the time, The Monitor reported, countries like USA, Britain, Tanzania, Kenya, South Africa and other international groups were talking to both sides of the divide to see that the situation doesn’t worsen.

Museveni, Kagame meet
The two leaders—Museveni and Kagame—had been expected to meet and hold talks in Gabarone, Botswana. Aides to both leaders gave varying reasons on why the meeting did not take place, including it not being scheduled.
On November 6, 2001, more than two months after Museveni’s letter, the two leaders met in UK.
Former British Prime Minister Tony Blair and Ms Short convened the meeting, which sought to address the concerns raised by Ugandan and Rwandan authorities.
The media, including The Monitor, took a central role in not only informing the world what was going on, but also facilitating propaganda on both sides of the divide.

Take, for example, a November 26, 2001 cover story by The Monitor “Rwanda angered, vows to spill beans”, which carried a reaction by the Rwandan government to a 14 page statement by Mr Mbabazi published by Sunday Vision the previous day.
In his statement, Mr Mbabazi had given some details of what transpired in the London meeting, accused Rwanda’s director of cabinet, Dr Theogene Rudasingwa, of giving a statement about the same meeting that contained falsehoods, and concluded that there were deeply rooted problems between the two countries that needed to be solved.
For example, Mr Mbabazi, retaliated that Uganda had evidence that Rwanda gave financial support to Dr Besigye and singled out then Col Patrick Karegyeya, who he said gave money to Dr Besigye. Col Karegyeya would later fall out with Kigali and flee the country. The Ugandan-born ex-Rwandan intelligence chief was in December 2013 assassinated in Johannesburg, South Africa.
Dr Rudasingwa, who had accused the Ugandan authorities of treating Rwanda as “a student”, which he said was “unacceptable”, maintained his government stood by what he had said. He threatened to make public what had been happening, at least from Rwanda’s view. The conflict was far from over.
Years later, in 2011, there was a reporting of cooling of tensions between Kagame and Museveni, Rwanda and Uganda. In 2015, President Museveni visited Rwanda and donated $200,000 (about Shs720m) towards the construction of Ntare School in Rwanda. Both men are Old Boys of Ntare School in Uganda.

Museveni’s letter (August 28, 2001)
Rt. Hon. Claire Short, salutations from your friends in Uganda. I hope your trip around the Great Lakes region was pleasant and fruitful.
I am embarrassed to have to communicate with you about the deteriorating situation in the bilateral relations between Uganda and the government of Rwanda, led by president Kagame.
We have no doubt that Rwanda is planning aggression against us either using proxies or, even, directly. There are some Ugandan army officers who ran from here, jumping bail or fleeing potential prosecution for a number of crimes, to Rwanda.
Since some months these officers, who we hear were given amnesty in Rwanda, have been frantically telephoning many serving army officers in Uganda asking them to betray their country by spying for Rwanda and fighting our government and people.
Furthermore, they have been recruiting Ugandan youth and taking them to Kigali for military training. We are now sure that they have opened three training centres around Kigali with the full support of the Rwanda government. We hear that they have also opened another centre for the same purpose in Rutshuru, a part of eastern Congo they control.
Meanwhile, their intelligence is very aggressively inquiring about the strength of various army units of ours and so on.

You remember, just before you came, I went to Rwanda and met Mr Kagame at the border, on the Rwanda side. In that meeting we agreed that the dissidents of the two countries entering either country should not be supported by the host government, but they should also not be allowed to carry out any hostile activities against their home country.
The prohibited activities included propaganda, not to mention military training and spying. Unfortunately, the Rwanda government is doing the exact opposite.
I had hoped to talk to Mr Kagame in Arusha and in the recently concluded SMART Partnership meeting that took place here. As Mr Kagame did not come to either, I managed to talk to him only on telephone. I am soon sending our Foreign minister to raise these matters again.
Right honourable minister, we have just defeated the protracted terrorism organised against us by Sudan, both in the west of Uganda and in the north.
We cannot countenance nor tolerate another round of terrorism this time organised by Mr Kagame whom we sacrificed so much to stand with when the whole world was either against their cause or indifferent to it.
I am, therefore, writing to you for two reasons:
1. First of all, to inform you about the sad and childish developments here which, nevertheless, are very grave for this region.
2. Secondly, to request you to show understanding to our Intention to raise our defence spending beyond the 1.9% of GDP we had agreed with the donors.
You remember, I have always held the view that given the instability of this region, it is naive and inviting trouble to underspend perennially on defence. 1.9% of GDP has, recently, been translating into about US$110 million per annum.
This figure could be alright if we had finished the capital development of our army involving training of officers, NCOs and technical staff (pilots, rank crews, artillery crews, etc.); buying or making arrangements to receive requisite equipment in case of conflict given this unstable region with all sorts of adventurers with distorted concepts about society; and building barracks for our army to have decent accommodation.