The WHO is under the control of the Illuminati, which utilizes the WHO's resources to carry advance its agenda. In the 2020s, Elizabeth DuClare, a member of the Illuminati Council of Five, is the spokeswoman and de facto head of the organization.
In 2008, the World Health Organization began the construction of Omega Ranch as part of their "Disease Control Initiative." This facility was created to reasearch viral genetics and biological sciences. The facility greatly suffered due to underfunding and staffing problems. These issues eventually resulted in "The 2018 Incident" when a containment breach occured. This breach saw the release of a modified version of the H5N1 avian flu virus. The WHO were forced to close the facility when the spread of the virus resulted in the deaths of tens of thousands of people. Despite this catastrophic incident, Omega Ranch reopened in 2021. A World Health Organization monument is located in Omega Ranch, implying that WHO is still affiliated with the research center.
In 2027, the WHO assigns health inspector Stuart St. John to investigate clinic trials of the drug Riezene. When the inspector discovers that the drug is unsafe, the WHO turns a blind eye on the matter. The inspector is later assassinated on behalf of the Illuminati.
Later in 2027, the Illuminati utilize the WHO to implement a scheme known as the "biochip initiative." Their plan is to distribute a biochip specifically designed to allow the Illuminati to control mechanically augmented people. When the biochips are ready, DuClare gives a statement urging augmented people to visit their nearest LIMB clinic to replace their "malfunctioning" biochip with the chips designed to give the Illuminati control over the augmented population. The plan goes awry as a result of Hugh Darrow's actions, culminating in the Aug Incident.
After the Aug Incident, the WHO sets up clinics with the stated purpose of helping augmented people reintegrate with society. One of such clinics is Facility 451, which Adam Jensen observes to be more akin to an asylum rather than a clinic.