General Minihan came to DIA in the midst of critical events in the Balkans. In the summer of 1995, the Croatian Army launched several successful offensives in the Krajina region, NATO launched air strikes against targets in Bosnian Serb territory, and Bosnian Serb forces overran Srebrenica, a UN declared "safe area." In the fall on 1995, the major players in the Yugoslav crisis agreed in Geneva on the basic principles for peace in Bosnia. The agreement led to the signing of the Dayton Peace Agreement in November. DIA supported the NATO-led Implementation Force (IFOR) commitment to Bosnia with three National Intelligence Support Teams (NISTs) and the Pentagon-based Yugoslav Intelligence Task Force (ITF).

The newly formed Defense HUMINT (Human Intelligence) Service (DHS) achieved its initial operating capability on 1 October 1995. DHS consolidated the HUMINT activities of all the Services under the umbrella of DIA. This new organization reflected the driving need to consolidate and focus downsized resources to maximize the effectiveness of reduced assets. DIA was also designated as the Intelligence Community's executive agent for Measurement and Signature Intelligence (MASINT).

In November 1995, the Department of Defense consolidated imagery and mapping functions into the National Imagery and Mapping Agency (NIMA). It incorporated all of the Central Imagery Office and the Defense Mapping Agency, as well as portions of the National Photographic Interpretation Center, the National Reconnaissance Office, the Defense Airborne Reconnaissance Office, and the imagery personnel and services in DIA. NIMA was formally established on 1 October 1996.

General Minihan's time at DIA was limited. The Secretary of Defense and the Chairman of the Joint Chiefs had agreed that General Minihan would serve at DIA only until February 1996, when he became the director of the National Security Agency.

In an historic event, the North Atlantic Treaty Organization took in three new members from the former Warsaw Pact military alliance in 1998: Hungary, Poland and the Czech Republic. Terrorists detonated bombs at the US Embassies in Kenya and Tanzania on 7 August 1998, killing more than 250 people, including twelve Americans. Islamic fundamentalists under the leadership of Osama bin Laden were suspected in the attack. In response, the US launched cruise missile strikes against "terrorist-related" bases in Afghanistan and Sudan on 20 August 1998. DESERT FOX was undertaken in December 1998, a seventy-hour air campaign in response to Iraq's barring of weapons inspectors.