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.