Nanyuki, Kenya, where residents have protested plans for a U.S.-backed Ebola quarantine facility near Laikipia Air Base. Photo by Martin Kithinji Mwirigi/Wikimedia Common

NAIROBI, Kenya — On June 1, 2026, hundreds of people flooded the streets of Nanyuki, a quiet town in Laikipia County about 200 kilometres north of Nairobi, to protest a proposed U.S.-backed Ebola quarantine facility at Laikipia Air Base. By the end of the second day of demonstrations, two people had been killed after police opened fire on protesters, including one near the perimeter of the air base.

The protests began at around 9 a.m. outside Quickmart Supermarket in Nanyuki, before spreading through the town as shops closed, streets emptied, and schools shut their doors. Protesters, many of them young people, marched chanting anti-government slogans and demanding an immediate halt to the project. Some lit fires and hurled stones at law enforcement officers, while police deployed water cannons and tear gas to disperse the crowds.

The trigger for the protests was a plan, confirmed by senior Trump administration officials, to establish a 50-bed Ebola quarantine facility at Laikipia Air Base for Americans exposed to the virus in Central Africa. Rather than allow exposed Americans in the region to return home, U.S. Secretary of State Marco Rubio said during a Cabinet meeting that “we cannot and will not allow any cases of Ebola to enter the United States.” Kenya became the alternative, with U.S. officials saying the facility would be staffed by personnel from the U.S. Public Health Service, even as Kenyan officials pushed for the site to serve people of all nationalities. For many residents in Nanyuki, the question was not only whether the facility was safe, but why their town had been chosen as America’s Ebola containment site.

The proposed facility was tied to an Ebola outbreak that had begun weeks earlier in eastern DRC, where the World Health Organization (WHO) received an alert on May 5, 2026, about an unknown illness with high mortality in Mongbwalu Health Zone, in Ituri Province, a high-traffic mining area less than 500 kilometres from Uganda. The virus was later identified as the Bundibugyo strain, a rarer form of Ebola. On May 17, WHO Director-General Tedros Adhanom Ghebreyesus declared the outbreak a Public Health Emergency of International Concern. As of June 15, the European Centre for Disease Prevention and Control reported 837 confirmed cases in the DRC, including 196 confirmed deaths, with Ituri remaining the most affected province.

Kenya has so far recorded no confirmed Ebola cases, which made the proposed facility more difficult for many residents to accept. Because there are no licensed vaccines or specific therapeutics against the Bundibugyo strain, containing the outbreak depends heavily on isolation, contact tracing, and cooperation from affected communities. A secretive arrangement designating a country with no confirmed cases as a holding site for Americans exposed to Ebola elsewhere has strained public trust, especially when the country being asked to absorb the risk has fewer resources to manage imported cases.

The Katiba Institute, a constitutional rights organization, filed an urgent legal challenge over the proposed facility, citing a lack of transparency, public participation, and parliamentary oversight. In its petition, the institute asked the court to determine whether the executive could expose the public to significant health risks without first complying with constitutional safeguards. The Katiba Institute, a constitutional rights organization, filed an urgent legal challenge over the facility, citing a lack of transparency, public participation, and parliamentary oversight. In its petition, the institute asked the court to determine whether the executive could expose the public to significant health risks without first complying with constitutional safeguards.

The Law Society of Kenya, a legal professional body, also asked the court to nullify any agreements between Kenya and the United States over the project, citing public health risks, a lack of public participation, and Kenya’s lack of the high-containment infrastructure required to safely manage such a facility. The Kenya Medical Practitioners, Pharmacists and Dentists Union (KMPDU) publicly opposed the facility from a public health standpoint. In a May 28 statement, KMPDU said, “We will not sit back and watch Kenya be treated as a containment colony for a lethal pathogen that we did not generate.”

High Court Judge Patricia Nyaundi later issued interim conservatory orders barring the government from building or beginning operations at the facility, and ordered it to disclose all agreements and operational protocols before the next hearing on June 23. Despite the court order, Reuters reported that U.S. equipment and personnel continued arriving at the site with the backing of Kenyan authorities, though Health Cabinet Secretary Aden Duale later said the government had suspended the project and would comply with the court.

On June 1, President William Ruto defended the proposed facility, telling reporters, “We are a responsible government. We know what we are doing.” He framed the project as part of Kenya’s broader Ebola preparedness plan and its long-standing health partnership with Washington, saying it would serve both Kenyans and foreign nationals.

A second round of demonstrations erupted on June 9, when another person was shot dead as police again deployed water cannons and tear gas against protesters. The death toll from the two rounds of protests now stands at three, with more than 10 protesters arrested.

The High Court is expected to revisit Katiba Institute’s legal challenge on June 23, when the government must disclose the agreements and operational documents behind the proposed facility. If it fails to do so, the interim conservatory orders could be extended.

Marco Rubio later softened his earlier position, telling a Senate Appropriations subcommittee on June 3 that the facility was intended for observation and calling the controversy a “misunderstanding.” The United States has not issued a formal statement on the deaths in Nanyuki or clearly confirmed whether the facility would serve non-American patients, as Ruto has claimed.

Author Bio: Chesang Rotich is a climate and sustainability professional working at the intersection of public policy and sustainable finance across East Africa and the United States. She is currently based in Nairobi, where she writes on climate, energy, and the politics of development across the continent.