After a year in limbo, the Navy has decided to move ahead and replace the service's top intelligence officer, whose tenure has been hamstrung by suspected ties to a disgraced defense contracting firm.

The Office of the Secretary of the Navy has nominated Rear Adm. Elizabeth Train for a third star and to relieve Vice Adm. Ted Branch as director of naval intelligence, according to two Navy officials.

Branch's access to classified information was suspended in November 2013, along with that of a deputy, Rear Adm. Bruce Loveless, the director of intelligence operations, for possible connections to Glenn Defense Marine Asia — the husbanding firm at the center of one of the Navy's biggest bribery scandals in decades.

Since then, Branch has been limited to personnel management functions and leading an initiative to raise the profile of cyber security in the fleet, amid a growing sense of dysfunction in the intelligence community. Both men remain in their positions.

Navy Secretary Ray Mabus made the call to nominate Train, a career intelligence officer who commands the Office of Naval Intelligence and directs the National Maritime Intelligence-Integration Office, because there has been no indication from the Justice Department as to when the investigation might wrap up, according to a senior Navy official familiar with the personnel decision.

Branch, in his first public statement about his predicament, confirmed Train's nomination in a statement to Navy Times.

"I have been advised that this nomination is going forward now because my access to classified information has been restricted as a result [of] an ongoing investigation concerning work performed by Glenn Defense Marine Asia during my command of the aircraft carrier Nimitz ten years ago," Branch said in the Nov. 26 statement. "I am disappointed, as I have always hoped and expected that my classified access would be restored so that I can continue as the deputy CNO for information dominance and director of naval intelligence. The investigation has been pending for over a year, and I welcome its conclusion so that I can resume in full my service to the Navy and the country."

Mabus decided to nominate Train after his concern that Branch's temporary suspension has now passed a year, with no end in sight. That's forced Branch to miss important meetings where classified information was being shared, and left the Navy intelligence community feeling underrepresented during briefings with the three-star heads of intelligence from the other services.

"[Mabus sees] the need to have an experienced officer in this key position who is able to address the full spectrum of the duties required," the senior official said.

The official went on to say that the secretary's decision had nothing to do with any new evidence or information regarding Branch's guilt or innocence. Indeed, officials have told Navy Times that the Justice Department's source may have confused Branch with another officer and that the lack of any charges against Branch made the decision to replace him especially difficult.

Mabus will withdraw Train's nomination if Branch is cleared of charges between now and when Train is confirmed, which Navy officials estimate will take place in early 2015 after the new Congress is sworn in, the official said. If Train is confirmed and relieves Branch next year, it's possible he would have to retire as a two-star, but a final determination on that would come later.

Train is a career intelligence officer who is currently the commanding officer of the Office of Naval Intelligence. She has previously served as the intelligence chief at the Office of the Chairman of the Joint Chiefs.

Fat Leonard

Branch and Loveless lost their clearances while the Justice Department investigated their connections to GDMA and its larger-than-life CEO, Leonard Glenn Francis, who is accused of bribing Navy officers to steer ships to ports where he allegedly bilked the Navy with overcharges and bogus fees.

It has been among the most high-profile corruption scandals in years, with active-duty officers criminally charged or fired from their positions in a wide-ranging investigation that could implicate dozens. Francis, known as "Fat Leonard" for his corpulence, was a fixture of WESTPAC cruises as the head of 7th Fleet's lead husbanding firm, responsible for arranging port services for visiting ships.

In return for gifts and junkets, prosecutors allege Francis expected information from his active-duty contacts, some of which, like ship's schedules, for example, was classified. He also allegedly prodded them to reroute ships to unusual ports where he could overcharge the service undetected. Francis has pleaded not guilty.

Navy officials say Branch is not suspected of leaking classified information. But he reportedly has been investigated for accepting gifts from Francis, which could open him up to blackmail. Branch, a career F/A-18 pilot who goes by the call sign "Twig," led the Nimitz from 2004 to 2007. He commanded the flattop during its 2005 Western Pacific deployment that included stops in Malaysia, Guam and Hong Kong.

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