He served in the NATO chain of command as a deputy to the Supreme Allied Commander Europe, General Wesley Clark. In this capacity, he is best known for refusing, in June 1999, to block the runways of the Russian-occupied Pristina Airport, to isolate the Russian troops there.^[1] Had he complied with General Clark's order, there was a chance the British troops under his command could have come into armed conflict with the Russians; doing this without prior orders from Britain would have led to his dismissal for gross insubordination. On the other hand, defying Clark would have meant disobeying a direct order from a superior NATO officer (Clark was a four-star general; Jackson only a three-star). Jackson ultimately chose the latter course of action, reputedly saying "I won't start World War III for you",^[1] though the point became irrelevant when the American government prevailed upon the Hungarians, Romanians, and Bulgarians to prevent the Russians from using their airspace to fly reinforcements in.

Details of Russia's surprise occupation of Pristina airport at the end of the Kosovo war are revealed in a new BBC documentary on the conflict.