The music video for "What I've Done" explores the many ironies of humanity and its ill effects on the earth and the environment. It juxtaposes various pieces of footage: a large, well-fed man eating fast food, a woman measuring her waist and a man who is so malnourished that his ribcage is visible through his skin; African Americans being hosed down and the Ku Klux Klan; nuclear explosions, the World Trade Center towers collapsing, children waving American flags, a Middle Eastern child holding an AK-47, clips of oil tankers torn in half and birds covered in an oil slick. The band's turntablist Joe Hahn directed the video for the single, which was shot in the California desert. The video premiered on April 2, 2007 on MTV and Fuse. It premiered on MTV-Asia, MTV-Germany, TMF Netherlands and Canada's MuchMusic on April 3, 2007.

It features footage of the band performing in the desert, interspersed with stock footage reflecting on a variety of social and environmental issues including pollution, global warming, racism, Nazism, the Ku Klux Klan, abortion, homosexuality, starvation, terrorism, warfare, deforestation, poverty, drug addiction, obesity, destruction, rising gasoline prices and crimes committed by humanity. The video also features short views of important historical figures, such as Mother Teresa, Abraham Lincoln, Robert Kennedy, Fidel Castro, Saddam Hussein, Joseph Stalin, Adolf Hitler, Benito Mussolini, Mao Zedong, and Mahatma Gandhi. Some cut scenes like the traffic scene and the napalm exploding were also featured on the Rise Against music video for Ready To Fall.