On 9 October 2001, following the North Atlantic Council's decision on implementation of Article 5 of the Washington Treaty as a consequence of the 11 September 2001 attacks against the United States, NATO's STANAVFORMED was ordered to deploy to the Eastern Mediterranean to provide NATO presence in the area while demonstrating NATO's resolve and solidarity (Operation Active Endeavour).

Two weeks later Admiral Gregory G. Johnson, U.S. Navy, succeeded Admiral James O. Ellis, U.S. Navy, as Commander-in-Chief, Allied Forces Southern Europe. In his inaugural speech he challenged the AFSOUTH personnel to set aside all thinking and to concentrate on innovative approaches. He said "we must not be a reactionary force frozen in old and comfortable ways of doing things; rather, we must bean engine of innovative leadership that leads AFSOUTH and NAVEUR to effective solutions."

While US-led operations were in progress in Afghanistan, NATO assured sustainability to Operation Active Edeavour by bring into the Mediterranean NATO's Standing Naval Force Atlantic. This operation proved also to provide the area with a number of secondary positive effects. Search and rescue operations were conducted and NATO ships provided life-saving support to the crew of an oil rig and to the passengers of a sinking ship in the Eastern Mediterranean. But it would be only over time that the positive fallout of NATO's presence would appear evident. Notwithstanding the many NATO and national operational commitments, to retain operational readiness and interoperability of remaining forces was still a high priority. On 21 May-6 June 2002 NATO's bi-annual land, maritime, amphibious and air exercise Dynamic Mix 2002 (DM02) took place in Spain (including the Canary Islands), the Western Mediterranean, the Southeast Atlantic and Turkey. Later on , on 17-28 June 2002, Exercise Cooperative Best Effort 2002 was conducted in in T'bilisi, Georgia. And NATO's annual maritime and amphibious exercise Cooperative Partner 2002 took place near Constanta, Romania, and in the Black Sea on 21 June-6 July 2002. To complete the yearly training program, ten NATO nations and twelve Partner nations joined forces in Exercise Cooperative Key 2002 in Saint-Dizier, France on 22 September-4 October and the annual amphibious, maritime and power projection exercise Destined Glory 2002 was conducted in the Tyrrhenian and Ionian Seas on 5-15 October 2002.

A third priority of AFSOUTH, after current operations and training, remained cooperation and dialogue, both within PfP and the Mediterranean Dialogue. The Headquarters had therefore to manage the schedules so as to deconflict all the programs. As an example of this, NATO naval forces conducted a number of port visits to ports in the Black Sea and the Mediterranean, to include ports of the Mediterranean Dialogue countries. A conference to discuss prospects for further development of NATO's Mediterranean Dialogue program was held at RHQ AFSOUTH in October, with participation of senior representatives from Algeria, Jordan, Mauritania, Morocco and Tunisia.

• NATO would remain committed to security and stability in the Balkans;
• the restructuring of the NATO and NATO-led forces would reflect the progress achieved in building self-sustained stability;
• the new structure would enable SFOR and KFOR to meet remaining challenges more effectively and efficiently.

Another important concept behind the harmonization of theater activities was the acknowledgment that each mission had specific challenges, tasks and objectives and their distinct mandates would remain.

In Bosnia, it was decided SFOR would reach a force strength of about 12,000 by the beginning of 2003, with three multinational Brigades each of which commanded by a Brigadier and containing distinct Battle Groups (BGs). These BGs would be multinational and essentially reinforced battalion task forces with their own organic capabilities. In addition, there would be dedicated Tactical Reserve Forces able to intervene anywhere within the Theatre of Operations. These could in turn be augmented by the Operational Reserve Force, which is principally composed of Over The Horizon Forces.

Similarly, KFOR Multinational Brigades were reduced to four, with total force to be progressively reduced to 32,000 by the end of 2002.

• Commanding all NATO and NATO-led Forces in the country;
• Supporting KFOR and ensure KFOR Line of Communication in the country, to include the coordination of the activities of the National Support Elements;
• Facilitating the exchange of releasable information and data, assist and coordinate Bi-Lateral support and military cooperation with General Staff, Ministry of Defense, Ministry of Interior and other Governmental entities as deemed appropriate by NATO and Government authorities;
• Liaise with other international organizations;
• Working in close co-operation with the NATO Ambassador/Civil Liaison Officer, conducting liaison directly with the Government authorities as appropriate

Durres, 5 Aug. 2002 - Albanian President Alfred Moisu, thanking Brigadier General Umberto Caparro, the first Senior Military Representative (SMR) and Brigadier General Franco Giannini taking over at the presence of Admiral Gregory G. Johnson, CINCSOUTH.

Albania also continued to play a vital role in maintaining stability in the Balkans. It became clear that NATO's relationship with the Albanian government and the military should reflect this importance. In order to achieve this, on 17 June 02, NATO transformed the former KFOR Communication Zone WEST into a NATO Headquarters in Tirana (NHQT), commanded by a Senior Military Representative (SMR), to report directly to the Commander-in-Chief Allied Forces Southern Europe. Commanded by the SMR, the NHQT was to facilitate co-ordination between the Government of Albania, Organisations of the International Community and NATO He was also tasked to monitor lines of communication and support Commander KFOR (COMKFOR) and the SMR in Skopje.

At the beginning of the summer of 2002 AFSOUTH was therefore engaged in supervising five major 'out-of-area' operations or missions: SFOR, KFOR, NHQS, NHQT and operation Active Endeavour. Embedded in the mission of NHQS there was indeed another operation, named "Amber Fox”, which had started on 26 September 2001.
Troops from Task Force Fox during an exercise in Opae, Kumanovo

The mandate of "Amber Fox" was to provide additional security to International Community monitors in the crisis areas, while government authorities had primarily responsibility for their security. The end of "Amber Fox" mission was a remarkable example of how joint efforts of the International Community and the authorities of the former Yugoslav Republic of Macedonia(2) resulted in bringing the country from the brink of civil war back on the track of further democratization and improvement of human rights through a process of dialog and reconciliation. As a result of the greatly improved security in the country, local authorities and NATO decided to bring the mission to an end on 15 December 2002 when the last extension of the NATO mandate expired. In order to demonstrate its commitment and support, NATO, by invitation of the Government of the former Yugoslav Republic of Macedonia(2), started a new mission called " Allied Harmony”. The executive command of the new mission was given to the NATO Headquarters Skopje. The forces were also reduced from about 700 soldiers to about 450 while at the same time NATO kept almost the same number of liaison teams on the ground.

NATO Heads of State and Government met in Prague on 21 November 2002 and approved the design for a transformed Alliance, open to new members, with a structure oriented towards new operational capabilities and able to meet new challenges and project stability through enhanced cooperation and dialogue -- to include upgrading substantially the political and practical dimensions of the Mediterranean Dialogue. AFSOUTH may have well presented them a model on which to build. Indeed, the principles on which the future military structure of the Alliance was to be designed reflected many of the realities and lessons learned of the Southern Region for several years.

The profound transformation decided at the Prague Summit committed NATO headquarters to assign top priority to the transition into a new command structure, the adoption of new missions and the development of new capabilities. However, the very reason why those decisions had been taken -- growing world instability -- soon reached another peak with the situation which led to the beginning of the US Operation Iraqi Freedom.

Almost at the same time, the NATO Defense Planning Committee authorized the allied military authorities to urgently implement defensive measures to assist Turkey. Two NATO E3-A AWACS Early Warning Aircraft arrived at Turkey's Konya Air Base on 26 February, and immediately started missions to provide surveillance and early warning for defensive purposes, in order to maintain the integrity of Turkish airspace.

Eventually, AFSOUTH also assumed control of three Dutch batteries of Patriot ground-based, air defense missile systems, which received additional enhanced missiles provided by the German Air Force and deployed to Diyarbakir and Batman, South Eastern Turkey. Two additional U.S. Patriot batteries were eventually deployed to Turkey.
The Supreme Allied Commander Europe (SACEUR), General James L. Jones, approved on 13 March 2003 the plan for Operation "Display Deterrence", the nickname given to NATO's contribution to the defense of Turkey. The Commander-in-Chief AlliedForces Southern Europe, Admiral Gregory G. Johnson, US Navy, was appointed Joint Force Commander. On 16 April 2003, the North Atlantic Council (NAC) agreed to conclude its formal consultations on Turkey's security under Article 4 of the North Atlantic Treaty. The decision was taken on the basis of NATO military and other assessments and advice, and Turkish concerns.

In response to that decision, on 16 April 2003, General Jones ordered the gradual reduction of NATO AWACS crews, the Patriot Fire Units, and other support personnel deployed to Turkey. By that date AWACS crews had flown about 100 missions and more than 950 flying hours. Overall, NATO had committed over 1000 technically advanced and highly capable forces.

Operation Display Deterrence was formally terminated on 30 April 2003, just one day after Task Force Endeavour began boarding operations following a NAC decision to enhance the effectiveness of the naval operations against suspected terrorist activities in the Mediterranean. The boarding operations were to be of a compliant nature and conducted in accordance with the rules of international law.

While the AFSOUTH staff was hastily working at defining plans for the transition into the new command structure, normal operational commitments continued relentlessly. Operations in the Balkans remained an important focus while SFOR and KFOR, also because of the progressive reduction in the deployed forces, continued to maintain a visible NATO commitment to the safe and secure environments required for Bosnia and Kosovo. This commitment became even more visible with the operational rehearsal "Dynamic Response 03,” conducted in Bosnia-Herzegovina and Kosovo from 26 August to 24 September 2003. This annual rehearsal proved NATO's ability to significantly reinforce in-theatre, NATO-led forces with so-called "Over-The-Horizon-Forces,” at short notice.

Traditionally, military training activities are not permitted to interfere with operations, but they are, nonetheless, essential to maintain the required effectiveness and interoperability of NATO and Partner forces. During 2003, AFSOUTH conducted or directed exercises Dog Fish, the world's largest annual anti-submarine warfare exercise which took place in the waters of the Ionian Sea to east of Sicily, 20 February until 05 March 03; Cooperative Best Effort, a land-based PfP exercise which took place in Armenia from 16 to 27 June 2003 (the first PfP exercise hosted by that nation and the first time that Russia participated in such a NATO exercise with staff officers and an infantry squad integrated into the exercise's multinational force structure; Cooperative Partner, PfP's annual maritime and amphibious exercise which took place from 20 June until 5 July 2003 near Odessa, Ukraine, and in the Black Sea; Cooperative Key, a PfP air exercise which took place from 01 to 13 Sep 03 in Plovdiv, Bulgaria; and Cooperative Engagement, NATO's biannual PfP maritime exercise, which took place from 13 to 20 Sep 03 near Split, Croatia, and in the Adriatic Sea.

But many more activities were also conducted in 2003 to pursue stability through dialogue and cooperation. Among these, particular significance was given to the visit on 20 November of Mr. Boris Tadic, Minister of Defense of the Union of Serbia and Montenegro, and General Branko Krga, Chief Defense of the Union of Serbia and Montenegro, at Headquarters AFSOUTH. This was the first visit of defense authorities of the Union of Serbia and Montenegro to the NATO Headquarters in Naples and was, as Admiral Johnson highlighted, "an important step in the continuing process of bringing peace and stability to the Balkans region.”