Arriving for a 2005 press conference in an arson case are Channing Phillips, a spokesman for the US attorney's office; (someone unidentified) and Kenneth L. Wainstein, U.S. Attorney for the District of Columbia. (Robert A. Reeder/The Washington Post)

President Obama has nominated a Justice Department official to become the District’s next top prosecutor, passing over the man who currently heads the largest U.S. attorney’s office in the nation.

Channing D. Phillips, 57, who previously worked as a prosecutor in the District, will come before the U.S. Senate. If confirmed, he will take over an office of more than 350 attorneys who prosecute complex terrorism and financial fraud cases, as well as drug and violent street crimes in the nation’s capital.

But among the biggest issues facing Phillips would be whether to continue the four-year corruption investigation into former D.C. mayor Vincent C. Gray. The process for choosing the new U.S. attorney was somewhat of a referendum on how the former top prosecutor, Ronald L. Machen — and then his right-hand man, current acting U.S. attorney Vincent H. Cohen Jr. — have handled the long-running investigation, according to two officials involved in the process.

During Machen’s term, the office came under scrutiny after prosecutors publicly accused Gray (D) of having knowledge of a “shadow campaign” to illegally funnel more than $660,000 into his 2010 get-out-the-vote effort. Gray has called the allegations “lies.”

Gray supporters were angered by the allegations, which surfaced as part of a plea deal made with a Gray donor that was announced only weeks before the former mayor’s loss in the 2014 Democratic primary.

President Obama nominated Channing D. Phillips, 57, on Thursday to become the next U.S. attorney for the District of Columbia. If confirmed, one of Phillips's initial challenges will be to decided whether to continue a corruption investigation into former D.C. mayor Vincent C. Gray. (WUSA9)

The U.S. attorney’s office had defended the timing of the investigation, saying that the office’s work was driven by evidence — not the election calendar. But as the probe has dragged on without the office charging or clearing the former mayor, criticism has intensified.

Former U.S. attorney Kenneth Wainstein, who was Phillips’s boss for a time, said having a new leader in the office would help provide a fresh perspective on the Gray investigation and other cases.

“I’m sure Channing will take a fresh, hard look at the Gray case, and he’ll end up doing what’s fair and just, without regard to any political dynamics or influences that might be at play in either direction,” Wainstein said.

Phillips said in a brief interview that he was “deeply honored” by the nomination but declined to comment further.

In a statement, Cohen said he would resign as of midnight Oct. 18 and that it had been “a great honor to serve the people” of the District.

“We have made great progress over the past five years in fighting violent crime, public corruption and threats to our national security,” Cohen said. “There are some important cases that I wish I could see through to their conclusions, but I have complete confidence in the team at the U.S. attorney’s office to follow through and do justice for the people of the District.”

Cohen’s supporters, including D.C. Attorney General Karl Racine, said they felt Cohen was not judged for the totality of his record. They cited Cohen’s work on violent crime investigations and the crackdown on synthetic drug use in the District.

“Vincent Cohen’s performance should be judged on its own as a top prosecutor in this city and should not be tied to anyone else’s,” Racine said.

But others said the Gray investigation needs to be resolved, one way or another. Former D.C. prosecutor Justin Dillon, who worked under both Machen and Phillips and is now a defense attorney, said he expected Phillips would make the case a top priority.

“Channing is a superb choice,” Dillon said. “I would expect one of the first things on his agenda would be to make a decision about whether the former mayor should be charged or finally told he will not be charged. It has taken the U.S. attorney’s office far too long to make that decision.”

Gray’s attorney declined to comment on Phillips’s selection.

Machen, who was travelling much of Thursday, congratulated Phillips and wished him well, saying he would be an excellent U.S. attorney. Machen also praised Cohen, saying, “He’s done a great job and is a committed public servant.”

Should he be confirmed, Phillips’s new job will be somewhat of a homecoming for the longtime prosecutor and District native.

Phillips started in the U.S. Attorney’s Office for the District of Columbia in 1994 when he was hired by former attorney general Eric H. Holder Jr., then the city’s top prosecutor. Phillips later became the public face of the office, acting as spokesman during high-profile cases including the slaying of District intern Chandra Levy.

In 2009, Phillips briefly served as acting U.S. attorney, including overseeing the prosecution of Washington Wizards star Gilbert Arenas, who pleaded guilty to felony gun possession following an altercation with a teammate. The following year, Phillips was passed over for the top spot, and Machen was appointed.

Phillips went to work for the Justice Department in 2010 as Holder’s senior adviser and has stayed on to work for Attorney General Loretta Lynch.

In a statement, Holder called Phillips “one of the smartest, most dedicated prosecutors I’ve worked with during my almost four decades of public service.”

Phillips was among six people nominated by the White House on Thursday to serve as U.S. attorneys. Dana J. Boente, current acting U.S. attorney for the Eastern District of Virginia, was picked to stay in that post.

Lynch praised the selections of Phillips and the other nominees.

“They have demonstrated time and again — through their brilliant work, unwavering dedication, and tireless service — that they are exceptionally prepared to advance the Justice Department’s mission on behalf of the American people,” Lynch said in a statement.

Phillips’s pick follows a months-long selection process. The committee that met with candidates in private meetings in early May recommended both Phillips and Cohen to Del. Eleanor Holmes Norton (D-D.C.).

In addition to Phillips and Cohen, a third candidate was interviewed by the committee for the position: Christopher Zampogna, 48, a former New York prosecutor who runs a Washington-based civil litigation firm.

In a statement, Norton said she had recommended Phillips as her top choice, noting his work both as a prosecutor and later in the Office of the Attorney General. She called him a “first-rate lawyer who brings deeper experience in the Office of U.S. Attorney for the District of Columbia than anyone who has held that office.”

The U.S. attorney for the District is the only office in the nation that handles both federal and local cases.

In addition to the Gray investigation, Phillips would inherit the case of Ahmed Abu Khatallah, who is accused in the 2012 attack on U.S. facilities in Benghazi, Libya, which killed four Americans, including Ambassador J. Christopher Stevens. The office also is preparing for a retrial of Ingmar Guandique, who is accused in Levy’s 2001 killing. Earlier this year, a judge granted Guandique a new trial after it was revealed that a key witness in the first trial had lied.

The office also is handling prosecutions related to a recent spike in violent crime in the District. Among those is the case of a man charged in the May slayings of Northwest Washington businessman Savvas Savopoulos, his wife, his 10-year-old son and the family’s housekeeper.

This story has been updated.

Juliet Eilperin, Spencer S. Hsu and Paul Schwartzman contributed to this report.