His earliest assignments for Time magazine took him to East Timor in 2000; and, in December 2001, he went into Afghanistan to cover the U.S. search for al-Qaeda. As preparations for the invasion of Iraq began in early 2003, Ware relocated to the Kurdistan area. Although he has gone into battles embedded with U.S. forces, he also travelled to insurgent camps and reported on their perspective of the war. His Time bylines include reports from Kabul, Kandahar, Fallujah, Tikrit, Tal Afar, Mosul, Samarra, Ramadi, and Baghdad.

In September 2004, while investigating reports that Abu Mousab al-Zarqawi’s nascent “al-Qaeda in Iraq” group was openly claiming control of the Haifa Street area of Baghdad, Ware was briefly held at gunpoint by fighters loyal to Zarqawi who had pulled pins from live grenades and forced his car to stop. The men dragged him from the car and stood him beneath one of the banners, intending to film his execution with his own video camera. By threatening them with immediate and violent retaliation, his local guides, including members of the Ba’ath Party, were able to win his release. Ware has stated that, had this happened only a few months later, when Zarqawi’s group had grown stronger, he would have been killed.

In October 2004, he was named Time magazine’s Baghdad Bureau Chief. He was embedded for the September 2005 assault on Tal Afar, and his harrowing video of the battle has been included in a Frontline documentary and a 60 Minutes report. When with CNN, he was partnered with Thomas Evans, who produced for Anderson Cooper.

On 18 October 2006, CNN aired a small portion of a videotape sent to Ware that showed snipers shooting at, and apparently killing, American troops. The video was a tape sent to CNN to which Ware added narration for the edited broadcast that showed American soldiers being stalked and eventually brought under fire by the shooters. After the news report was shown, White House Press Secretary Tony Snow accused CNN of “propagandizing” the American public. Representative Duncan Hunter, then-chairman of the House Armed Services Committee, asked Donald Rumsfeld to remove CNN embedded reporters following the airing of the news report, claiming that “CNN has now served as the publicist for an enemy propaganda film featuring the killing of an American soldier.”

In 2008, he revealed that, while embedded in Diyala Province in 2007, he filmed the shooting of a young Iraqi man, whom he described as “a legitimate target”, by U.S. soldiers. The shot did not initially kill the man, but no aid was rendered during the estimated 20 minutes it took him to die. Ware told the story to illustrate how dehumanising war is for military personnel as well as reporters.

In February 2011, Ware confirmed that he would not be returning to CNN. He later told an Australian newspaper that he has formed a film company, Penance Films, and has recently finished a documentary about his time in Iraq called Only the Dead, released in 2015.