Natynczyk attended the U.S. Army War College, and was subsequently appointed Deputy Commanding General, III Corps and Fort Hood. In January 2004, he deployed with III Corps to Baghdad, Iraq, serving first as the Deputy Director of Strategy, Policy and Plans, and subsequently as the Deputy Commanding General of the Multi-National Corps (Iraq) during Operation Iraqi Freedom. Natynczyk led the Corps' 35,000 soldiers, consisting of 10 separate brigades, stationed throughout the Iraq Theatre of Operations. He was later awarded the Meritorious Service Cross specifically for his combat efforts in Operation Iraqi Freedom January 2004 to January 2005.