The song's lyrics about storms and drowning came back to light after the events of Hurricane Katrina. In September 2006, it was announced that Green Day and U2 were to record a cover version of the song for charitable purposes. Digital cover for live version Digital cover for live version
To coincide with the U2 and Green Day recording of the, both bands performed it live during the Monday Night Football Pregame show of the New Orleans Saints versus Atlanta Falcons game on September 25, 2006. This was the first game in the Louisiana Superdome since it was heavily damaged by Hurricane Katrina in August 2005. The live performance of the song was later sold online to benefit Music Rising, a charity created by U2's The Edge in order to bring instruments and music programs back to New Orleans.
In the four song set, U2 and Green Day performed "Wake Me Up When September Ends" followed by a medley of the American folk song, "House of the Rising Sun" (which has been covered by The Animals), The Skids' "The Saints Are Coming" and U2's "Beautiful Day" as a seven-piece band, augmented by the Rebirth Brass Band, the New Birth Brass Band, Troy Andrews, and Big Sam Williams. The lyrics of all four songs were customized by singers Billie Joe Armstrong and Bono to commemorate the trials, tribulations, and successes that faced the city over the past year. Punctuating the 68,000 fans' first season-ticket sellout of the Louisiana Superdome in its 31-year history, the New Orleans Saints beat the Atlanta Falcons 23-3. Since then, the song has been played at Saints home games before they take the field. The live version of "The Saints Are Coming" was immediately made available for download purchase at Real Rhapsody.
The studio version of the song was released for digital download on October 30, 2006 and released as a CD single on November 6, 2006. The song also appears on U2's hits album, U218 Singles, which was released on November 20, 2006. The song was played for the first time with U2 alone on U2's re-debut of the Vertigo Tour in Brisbane, Australia, on November 7, 2006.
A music video for "The Saints Are Coming," directed by Chris Milk, was released on video site YouTube on October 27, 2006. The music video shows the two bands playing at the Abbey Road Studio and at the Louisiana Superdome (though the footage from the live performance at the Superdome has been overdubbed with the studio version of the song), intermixed with news footage of the displacement of residents after Hurricane Katrina in New Orleans. The second half of the video shows an alternate history in which George W. Bush redeployed troops and vehicles from Iraq to New Orleans to help victims of the hurricane, with the military personnel fulfilling the titular role of the "saints." In the words of the director, this was done to "make a commentary on the Katrina disaster ... from the standpoint of how things can and should be done in the future." The video ends with military support vehicles fading out as the camera pans to a sign that reads 'Not as seen on TV', alluding to the criticized response to Katrina while also parodying media deception on rescue coverage. The video had more than two million views on YouTube five days after its initial upload. The single has been given a Grammy nomination for "Best Rock Performance By A Duo Or Group". Billie Joe also recently performed the song with U2 in Hawaii at the end of the latter's Vertigo Tour.