Inside Story: A dive into Museveni’s spy network in Nairobi

For years, a weathered red box stored at Nyeri Primary School was the silent custodian of a harrowing tale: The Museveni family’s midnight dash to safety from the lurking shadows of abduction in November 1983.

This unassuming box, belonging to Museveni’s daughter Natasha, had been abandoned in the haste of their flight as her mother, Janet Museveni, scrambled to shield her family from a web of danger spun by both Ugandan and Kenyan operatives. At the time, her husband, Yoweri Museveni, was a guerrilla leader waging a fierce battle against the regime of President Milton Obote. The Museveni family was caught in the crossfire of a political struggle that spanned borders, with Ugandan authorities seeking to capture them as a way to neutralize their growing resistance.

The previous night, some 41 years ago, terror had knocked on Janet Museveni’s Nairobi hideout. The kidnappers, who had come under the guise of agents from Uganda’s intelligence, found only the housekeeper, John. They dragged him into the dark of the night, taking him across the border to Kampala. A neighbor, witnessing the unsettling event, had warned Janet: “Those people were looking for you.” Janet later recalled the sheer panic that gripped her. “That night I could hardly sleep. I was so anxious about the fate of John and the thought that if I had answered the door, I did not know where I would be,” she confessed in her memoir, My Life’s Journey.

It was a night of near-miss for Janet Museveni. The threat was palpable, and she had narrowly avoided capture, a realization she carried with her. Alongside John, who had been abducted, another dissident figure, Barak Kirya, leader of the Uganda Freedom Movement, was also taken that night. By morning, he was already handed over to Ugandan authorities across the border at Busia.

The Museveni family’s precarious escape reflected a time of overwhelming fear and danger, a period when Uganda’s internal strife echoed across borders and engulfed not just political leaders but their families too. Janet Museveni’s near-escape felt like divine intervention in hindsight, a providence that allowed her family to survive another night under the shadow of death.

At that time, she could only imagine the fate that awaited her if she had opened the door to those who sought to take her. And yet, despite her close encounter with abduction, she would go on to recount the experience in her memoir, providing insight into the deep anxiety that ruled her life during those tumultuous years.

Today, the tables have turned dramatically. Janet Museveni now resides in Uganda’s State House as the First Lady, alongside her husband, Yoweri Museveni, who has maintained his grip on power since January 1986. Ironically, as Uganda’s First Family, they now face accusations of terrorizing political opponents and allegedly employing mercenaries to abduct dissenters—a stark echo of the very tactics used by Milton Obote’s government against them in the early 1980s.

This week, the abduction of Uganda’s opposition leader, Kizza Besigye, has drawn chilling comparisons to the events of 1983. Besigye, a long-time critic of the Museveni regime, was seized in Nairobi and later transported to the Makindye Military Barracks, where he was presented before a military court martial. Besigye faces charges of illegal possession of a pistol, a weapon that has long symbolized resistance. His arrest echoes the old days when Museveni himself had begun his rebellion with nothing more than a single pistol tucked away beneath his jacket.

In his memoir, Sowing the Mustard Seed, Museveni recounted his guerrilla journey, which began with that very pistol. The firearm, always concealed beneath his jacket during secretive meetings with allies in Nairobi, was not just a weapon but a symbol of his struggle for freedom. The very same pistol that once represented the hope of a resistance movement is now the focal point of Besigye’s alleged wrongdoing. Besigye’s arrest and the charge of possessing a weapon are eerily reminiscent of the violence that shaped Uganda’s history and, in particular, the Museveni family’s own tumultuous rise to power.

Besigye’s abduction and subsequent transfer to military custody has raised questions about Kenya’s increasing role in the abduction of political figures, a troubling development that has led some to label Nairobi as a “kidnapper’s paradise.” The abduction of foreign nationals, including refugees, has been a rising concern, and Besigye’s case is just the latest in a string of high-profile disappearances. His situation casts a long shadow on the growing history of covert operations between Kenya and Uganda, as well as the wider East African region.

The abduction occurred under highly suspicious circumstances. On Saturday, Dr. Besigye and his associate, Haji Lutale, discreetly left their hotel in Kilimani, Nairobi, and hailed a taxi. Their destination was 108 Riverside Apartments, but unbeknownst to them, they were being closely watched. Their phones may have been compromised, or they were being tracked in real-time. Despite no visible signs of a struggle or commotion, their disappearance at the apartment complex suggested an operation executed with military precision. A statement by Martha Karua, a key figure in the political scene, confirmed their arrival at the building between 4:30 and 5:00 p.m., but that was the last time they were seen in public.

Kizza Besigye, once one of Yoweri Museveni’s most trusted allies, was an instrumental figure during the early days of the guerrilla movement. As Museveni’s personal physician, Besigye saved his life on several occasions. It was Besigye who, when Museveni collapsed from exhaustion during a difficult march, rushed to his side with life-saving rehydration salts. The bond they shared on the battlefield, however, would not survive once they transitioned to civilian life. Besigye’s decision to run against Museveni for the presidency in 2001 marked a definitive break in their relationship. Museveni, once his comrade, had become his adversary.

By 2001, Besigye had become a significant threat to Museveni’s hold on power. His call for multiparty democracy and fair elections drew the ire of the Museveni regime. He was imprisoned, placed under house arrest, and subjected to various charges—many of which were politically motivated. Besigye’s challenge to Museveni was seen as an existential threat, and as a result, he became a target for continued harassment, both legally and physically.

Besigye’s plight in Nairobi has drawn disturbing parallels to the past. In 1983, as Janet Museveni fled Uganda, she left behind her daughter Natasha’s box in Nyeri as she escaped. The same box, laden with memories of fear and loss, was left behind in the desperate scramble for safety.

Recalling the incident, Yoweri Museveni reflected in his autobiography, Sowing the Mustard Seed, on the absurdity of the situation. “In 1983, my family had to leave in a hurry because the government in Uganda wanted to kidnap my wife and children to punish me,” he wrote. “What useless outfits these African governments are, that they are threatened by a housewife and young children.”

Today, it is Museveni who is at the helm of a government that engages in high-profile abductions of political opponents. His regime has come full circle, employing the same methods of suppression he once fought against in his struggle for freedom. The irony is not lost on those who remember the Museveni family’s own escape from danger—and the box left behind in Nyeri.

The parallel stories of the Museveni family’s flight in 1983 and the abduction of Kizza Besigye today are reminders of the cycles of fear, repression, and political violence that continue to plague Uganda and the wider East African region. The lessons of history appear to have been forgotten, and the tactics that once terrorized the Museveni family are now employed by them to silence their opponents. It is a grim reflection of how power can warp over time and how the very tools of oppression once fought against can become the instruments of the ruling regime’s survival.