Justice Department Inspector General Glenn Fine noted in a report last week that restoring leadership and confidence in the department is a top priority, after the scandals that swirled around Alberto Gonzales.
"The department's removal of the U.S. attorneys and the controversy it created severely damaged the credibility of the department and raised doubts about the integrity of department prosecutive decisions," Fine noted in his report.
During Gonzales' tenure, the department ousted at least nine federal prosecutors, a move lawmakers from both parties said was unfair or, at worst, smacked of political motivation.
Fine also wrote, "The department must coordinate effectively with the department's new leadership to accomplish an orderly and efficient transition. In addition to continuing to restore confidence in the department over the long run, the incoming attorney general must address in a timely way the serious challenges facing the department."
In a joint opinion-editorial published last month, Leahy and Sen. Arlen Specter, R-Pa., the chairman and ranking member of the Senate Judiciary Committee, respectively, noted the recent problems that have plagued the department. "The flagship of our system of justice also faces a difficult road to rebuild trust after a crisis of leadership and conscience."
One pressing issue -- and a source of constant speculation -- is the future of the Guantanamo Bay, Cuba, detention center, which houses detainees classified by the United States as "enemy combatants."
Both Obama and his Republican rival, Arizona Sen. John McCain, said during the campaign that they supported closing the facility. Some legal experts have called for moving the detainees into U.S. criminal courts. But the idea of admitting evidence in connection with detainees who are still security threats and who have allegedly been tortured remains a delicate and complex legal issue.
During a briefing Nov. 11, Obama transition chief John Podesta said, "Sen. Obama has said that he intends to close the facility at Guantanamo. That's a complicated matter. It's under review."
Other major counterterrorism issues that may be considered sooner rather than later include a review of the FBI's investigative guidelines that were revised by current Attorney General Michael Mukasey early last month to establish one set of rules for the FBI in national security and criminal investigations.
In December 2009, the Justice Department will also face the expiration of two provisions of the USA Patriot Act; one section deals with roving wiretap authority for terrorism and espionage suspects who use multiple phone lines, the other with the so-called "library provision," which allows the FBI to obtain business records without judicial approval.
What's more, significant changes could come to the department's Civil Rights Division and the Environmental Natural Resource Division, which have largely enforced the use of consent decrees and sought settlements instead of prosecuting cases.
It is unclear if the 93 U.S. attorneys who serve at the pleasure of the president will have staggered resignations or if many will continue to serve as acting U.S. attorneys. Some, such as Patrick Fitzgerald in Chicago and David Nahmias in Atlanta, are career Justice Department officials who could stay on in the next administration.