In May 1994, Natynczyk embarked upon a year-long tour with the United Nations in the former Yugoslavia as Sector South-West Chief of Operations in Bosnia and Herzegovina within HQ 7 (UK) Armoured Brigade, then as the Chief of Land Operations, UNPROFOR HQ in Zagreb, Croatia. In June 1995, Natynczyk was assigned to the Vice Chief of the Defence Staff within National Defence HQ in Ottawa, Ontario. He then commanded his regiment for two years, leading the Dragoons during domestic operations in the Ottawa region during the 1998 ice storm. Natynczyk returned to Bosnia in 1998 as the Canadian Contingent Commander. On his return to Ottawa in March 1999, he was appointed J3 Plans and Operations during the period of deployments to Kosovo, Bosnia, East Timor and Eritrea.