President Bill Clinton announced on August 18, 1997, his intent to appoint Jones as U.S. Attorney for the Northern District of Alabama, and formally nominated Jones to the post on September 2, 1997. On September 8, 1997, the U.S. District Court for the Northern District of Alabama appointed Jones as interim U.S. Attorney. The Senate confirmed Jones's nomination on November 8, 1997, by voice vote. In January 1998, Eric Rudolph bombed the New Woman All Women Health Care Center in Birmingham. Jones was responsible for coordinating the state and federal task force in the aftermath, and advocated that Rudolph be tried first in Birmingham before being extradited and tried in Georgia for his crimes in that state, such as the Centennial Olympic Park bombing. Jones prosecuted Thomas Edwin Blanton Jr. and Bobby Frank Cherry, two members of the Ku Klux Klan, for their roles in the 1963 16th Street Baptist Church bombing. The case was reopened the year before Jones was appointed, but did not gain traction until his appointment. A federal grand jury was called in 1998, which caught the attention of Cherry's ex-wife, Willadean Cherry, and led her to call the FBI to give her testimony. Willadean then introduced Jones to family and friends, who reported their own experiences from the time of the bombing. A key piece of evidence was a tape from the time of the bombing in which Blanton said he had plotted with others to make the bomb. Jones was deputized to argue in state court and indicted Blanton and Cherry in 2000. Blanton was found guilty in 2001 and Cherry in 2002. Both were sentenced to life in prison. Blanton was up for parole in 2016; Jones spoke against his release, and parole was denied. Cherry died in prison in 2004. Jones recounts the history of the bombings and his subsequent involvement in Blanton and Cherry's prosecution in his 2019 book "Bending Toward Justice: The Birmingham Church Bombing that Changed the Course of Civil Rights". Jones left office in 2001 and returned to private practice. In 2004, he was court-appointed General Special Master in an environmental cleanup case involving Monsanto in Anniston, Alabama. In 2007, the Birmingham Civil Rights Institute gave Jones its 15th Anniversary Civil Rights Distinguished Service Award. Also in 2007, Jones testified before the United States House Committee on the Judiciary about the importance of reexamining crimes of the Civil Rights Era. In 2013, he formed the Birmingham firm Jones & Hawley, PC with longtime friend Greg Hawley. Jones was named one of "B-Metro Magazine"'s Fusion Award winners in 2015.