MSF was the only provider of medical care in Srebrenica as the violence intensified. MSF wondered if our role had become more like de facto prison doctors in the besieged city. Was MSF inadvertently contributing to the Bosnian Serbs' strategy of ethnic cleansing? Would calling for the evacuation of Bosnian Muslims actually result in aiding the Bosnian Serb’s ethnic cleansing policy of driving the people out and claiming the land? And what if Bosnian Muslims wanted to leave? What should the position of MSF have been?

Srebrenica fell to the Bosnian Serbs in July 1995 and approximately 8,000 Bosnian Muslim men and boys were massacred. How could this happen in the presence of United Nations (UN) peacekeepers in this so-called ‘safe zone’? What mechanisms did MSF put in place to speak out over the UN’s inability to protect the people of Srebrenica? 

Following the fall of Srebrenica, thousands were dead, missing or relocated to refugee camps. MSF questioned what could be done to ensure that peace did not take precedence over justice. Where did the responsibility for these actions and inactions lie?

Many nations were not taking responsibility for their (in)actions in the enclave. MSF France decided to put pressure on the French parliament to investigate France’s role in the fall of Srebrenica, by issuing an appeal for an investigative parliamentary commission. Should a humanitarian organisation speak out and advocate for official government inquiries in order to place responsibility, document events, seek justice and defend human rights?

As the instability of the region increases, MSF and other humanitarian organisations are eventually forced out of eastern Zaire entirely.  MSF suspects that thousands of refugees are suffering and at risk of dying. The organisation decides to launch an appeal for an armed international intervention and communicates about the plight of the population, predicting a health catastrophe, if access for aid agencies is not provided.

In November 1996, the offensive led by the ADFL and Rwandan forces empties the camps in eastern Zaire of their population. Some refugees were repatriated to Rwanda and others fled into the neighboring forest. MSF denounces the repatriation conditions and is reproached by the press for "catastrophic" forecasts made a few weeks earlier.

Finally allowed into South Kivu, a province in eastern Zaire, the MSF teams discover that refugees are being massacred by the ADFL and its allies, particularly in the Massisi and the Shabunda regions. MSF realises that MSF teams are used as bait by the ADFL to lure the refugees out of the forests and kill them.

The ADFL takes control of all of the Kivu province and refugees continue to flee their rapid advance eastwards through the forest.  MSF struggles to maintain access to the refugees amidst the violence, restrictions, and threats to team safety, while receiving continued reports about refugee massacres.

MSF's exploratory mission teams complete their reports on their Masisi and Shabunda visits. Details of mass graves, massacres, and the fact that the ADFL used humanitarian teams as bait to lure refugees out of the forests, sent shock waves through MSF offices. A debate about the use of the information collected ensued: should it be made public or not?

In May 1997, MSF published a new study describing the movements of refugees in the Great Lakes region of Africa and the fate of refugees. MSF planned to distribute the report to a small group of journalists, asking them not to cite MSF as the source of the information. However, a lack of communication between MSF offices and with the teams in the field, exacerbates tensions.

From mid-1997, MSF teams try to work together again. The organisation publishes retrospective studies that trace the odyssey of the Rwandan refugees through the Zairean jungle and contributes testimony to international investigations on human rights violations in the region.