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2003-2010: NATO's area of operations continues to expand

But NATO operations were gradually becoming more focused outside the Balkans and Europe. In Afghanistan it was becoming increasingly difficulty to organise and sustain the UN-authorised peacekeeping force (ISAF), so NATO agreed to take over responsibility for this force on 11 August 2003. Initially the scope of this operation was limited to the area around the capital Kabul, but during General Jones' tenure as SACEUR NATO gradually expanded its area of responsibility in response to requests from the UN and Afghan authorities, beginning with the northern part of the country in July 2004, then the west in June 2005. The greatest threats to Afghanistan's stability, however, lay in the south and east, where Taliban insurgents and drug producers/traffickers were concentrated. On 31 July 2006 the NATO-led ISAF expanded into southern Afghanistan, resulting in the heaviest ground fighting NATO troops had ever experienced, as the Taliban attempted to resist ISAF's presence and efforts to reconstruct the area. Then in October 2006 ISAF took over responsibility for operations in eastern Afghanistan, thus bringing the whole of the country into ISAF's Area of Operations.

In addition to commanding ISAF in Afghanistan, NATO has accepted responsibility for a training mission in Iraq, which was authorised in 2004 and continues to assist in the development of the Iraqi security forces with training courses both inside and outside Iraq. 2004 also saw NATO provide considerable assistance to the security of the Olympic Games and Paralympics in Athens, Greece, support that included NATO Airborne Early Warning (NAEW) aircraft. NAEW aircraft also supported security for the World Cup soccer competition held in Germany in 2006. NATO has also provided support to an African Union peacekeeping mission in Darfur, Sudan, from June 2005 until December 2007, primarily by organising and coordinating airlifts.

Humanitarian assistance was yet another important focus of NATO's operations during General Jones's tenure. After Hurricane Katrina caused widespread devastation in the southern United States at the end of August 2005, NATO responded positively to a US request for food, medical and logistics supplies. A second and much larger humanitarian assistance mission began in October, after Pakistan requested assistance to help it cope with the effects of a powerful earthquake that killed more than 73,000 people and left at least 4,000,000 people homeless, many of them in very remote areas. NATO quickly provided an air bridge for the concentration of relief supplies and then a highly effective airlift to bring them to Pakistan. These operations involved a total of 168 aircraft transporting 3,435 tons of assistance. NATO helicopters transported more than 1,750 tons of relief inside Pakistan and more than 7,650 sick, injured and displaced people. The NATO Field Hospital treated 4,890 patients, while mobile medical teams treated a further 3,424 patients. NATO engineers built 110 shelters and 9 schools while also clearing and repairing nearly 60 kilometres of road and removing large amounts of debris. NATO engineers also provided fresh water and repaired a permanent spring water distribution and storage system. This humanitarian assistance mission, which was greatly appreciated in Pakistan, ended in late January 2006.

During General Jones' tenure as SACEUR, the Alliance added seven new members – Bulgaria, Estonia, Latvia, Lithuania, Romania, Slovakia and Slovenia - bringing the total number of countries in the Alliance to 26. As an interim measure to assist some of these new members in securing their airspace, NATO nations have provided air policing.

On 7 December 2006 General Jones turned over command of Allied Command Operations to General John Craddock, United States Army. Afghanistan was naturally a key area of interest during General Craddock's tenure, because ISAF had taken over responsibility for the whole of the country just a few months earlier. He therefore oversaw the tremendous expansion of ISAF, both in terms of numbers and nations involved. Despite these increases, the situation in Afghanistan remained a serious challenge for the international community, as attacks by the Taliban and other militants continued to escalate, leading many observers to describe the overall situation as a stalemate. One important initiative of General Craddock was the decision to attack a major source of insurgent funding by having ISAF interdict drug trafficking and drug laboratories in Afghanistan, a policy that quickly began to show results

The Balkans also continued to be an important area of interest for General Craddock, as Kosovo and NATO's Kosovo Force (KFOR) both underwent significant changes. In Kosovo NATO had to deal with the challenges posed by that country's unilateral declaration of independence and the resulting stand-down of the Kosovo Protection Corps and the stand-up of the Kosovo Security Force. Another challenge for NATO in Kosovo came with the transfer of administrative responsibilities within the international community from the United Nations to the European Union. And for KFOR itself, General Craddock advocated and finally achieved political consent for the gradual transformation of the force to a much smaller Deterrent Presence.

In addition to providing the overall strategic direction for NATO's two major land-based operations in Kosovo and Afghanistan, General Craddock successfully deployed naval forces for operations against piracy in the sea lanes off the Horn of Africa, a continuing area of interest for NATO. And NATO's other maritime focus, Operation ACTIVE ENDEAVOUR in the Mediterranean, continued throughout his tenure as SACEUR.

Another key issue faced by General Craddock was the redesign of the NATO Response Force to reflect the actual operational tempo and the difficulty in generating sufficient forces, thus attempting to ensure the long-term viability of the NRF. Transformation was also a continuing subject during recent years, as NATO established two new transformational institutions under Allied Command Operations, the Intelligence Fusion Centre and the NATO Special Operations Coordination Centre. And on the international stage, General Craddock had to deal with tremendous fluctuations in the nature of NATO-Russia relations in the wake of the Georgia-Russia conflict of August 2008, a situation which began to return to normalcy just before General Craddock's departure with the decision to resume NATO-Russia Council meetings.

During General Craddock's tenure as SACEUR two more nations – Albania and Croatia – joined the Alliance in April 2009, bringing the total number of NATO members to 28. Once again, air policing is being provided by other NATO members until the new members develop their own capabilities.

On 2 July 2009 General Craddock was succeeded as SACEUR by Admiral James G. Stavridis, US Navy, in a ceremony marking a historic first in NATO's history – the first admiral to serve as SACEUR. In his first six months as SACEUR Admiral Stavridis has placed great emphasis on getting Allied Command Operations' message out ot a wide public using the new possibilities provided by social networking sites on the internet.  He has idenitifed new areas of concern for the Alliance such as cyber defense, the High North, and energy security, while continuing to carry out the existing NATO operations in Afghanistan, Kosovo and off the Horn of Africa.