Mabus often said that he would keep his job as long as Obama would have him. He oversaw the Navy and Marine Corps through the end of U.S. military operations in Iraq, the surge of tens of thousands of U.S. troops in Afghanistan, and advocated significant cultural shifts like the 2011 end of the “don’t ask, don’t tell” ban on gay service members serving openly.

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He also pressed to grow the size of the Navy’s fleet by dozens of ships, was a fierce advocate for the full integration of women in the military, and adopted policies to address climate change, even when some of those positions proved unpopular with Republican lawmakers or senior Marine Corps leaders.

“I think sort of across the board, there have been a lot of changes,” Mabus said in an interview this month in his Pentagon office. “But all with one goal in mind, and that’s making us a better Navy, making us a better Marine Corps, making us stronger and more able to do the job that needs to be done.

“Looking back — I’m looking for the right word,” he continued. “I’m very satisfied with where we are. That the changes we have made have, I think, made a difference, and made a difference in the right direction.”

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Mabus’s willingness to challenge those he disagreed with included a surprisingly public spat with senior Marine Corps leaders last fall as the military was considering opening all jobs to women for the first time.

The service, long seen as having misgivings about opening all combat jobs to women, released the results of a nine-month study that concluded the average woman was injured twice as often men, less accurate with infantry weapons and not as good at removing wounded troops from the battlefield. Mabus dismissed those results within a day, saying the Marine Corps not only did not delineate how the highest performing women could do, and that he saw no reason to keep grueling jobs like the infantry closed to women.

The argument over how to integrate women in the force continued after Defense Secretary Ashton B. Carter announced last December that he was opening all jobs across the military without exception, even though the Marines had requested to keep select jobs in the infantry and Special Operations closed to women. On Jan. 1, Mabus turned up the pressure, issuing a memo directing the service to respond within 15 days explaining how it would make all initial training coed.

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Marine Commandant Gen. Robert B. Neller and Mabus met shortly afterward and Mabus allowed boot camp to remain segregated. But the secretary’s actions prompted one Marine veteran in Congress, Rep. Duncan D. Hunter (R.-Calif.) to call for his resignation, citing Mabus’s alleged desire to “undercut the Marine Corps, distract it from its mission and insult its leaders.”

Other Republican lawmakers unloaded on Mabus in a blustery Senate Armed Services Committee hearing in February, questioning why the secretary was pushing the Marine Corps so hard.

“I do not think I have seen a more outrageous or ill-advised order from a service secretary to tell the Marines that they are going to take boot camp, which has been honed and put together for the benefit of the American people over decades, and you are going to tell them and order them to get a detailed plan within 15 days?” fumed Sen. Dan Sullivan (R.-Alaska), an infantry officer in the Marine Corps Reserve. “Is that even remotely possible?”

Hunter, asked about Mabus’s record this month, said the Navy secretary has “pushed the political ideology of Barack Obama to the extreme in the Navy.”

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“That encompasses a lot of things,” Hunter said. “Let’s just leave it at that. Let’s leave it there. Happy trails to Secretary Mabus.”

Mabus defended his emphasis on “developing a more diverse force,” noting that he also tripled the amount of maternity leave Navy Department personnel receive to 18 weeks and established new Reserve Officers’ Training Corps (ROTC) programs at schools ranging from Harvard University to Arizona State University. But he acknowledged he does not know whether any of those changes will be rolled back, and warned there will be negative consequences if they are.

“You make the decisions you think are right, right now, regardless what you think is going to happen in the future,” Mabus said. “But we are stronger because of this integration. That is undeniably true. So, if it gets rolled back, you’re weakening the United States military. You’re weakening the Navy. You’re weakening the Marine Corps. If that’s what you want to do, okay. But you have to be honest about it.”

Among Mabus’s other high-profile initiatives was a plan to get half of all the Navy’s fuel and power from non-petroleum sources by 2020 and to launch a “Great Green Fleet” in which all ships involved deployed without relying solely on fossil fuels.

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The effort, announced within months of him taking office, has faced scrutiny for years in part due to the costs of the biofuels the Navy has tested. Sen. John McCain (R.-Ariz.) cited the program in a report on a wasteful spending this month, noting that in a 2012 exercise, a blended fuel that included 50 percent biodiesel cost the Navy $26.75 per gallon, rather than the typical $3.25 per gallon.

In a more recent effort, the destroyer USS Mason was filled with biofuel that includes 5.5 percent palm oil and cost $1.99 per gallon. The Navy has characterized that as a success, with Mabus noting wryly that “I have not heard or seen people say, ‘Atta boy’ for finding a cheaper alternative.

“Ships don’t know when they’re getting biofuel now, or a mixture of biofuel and regular fuel,” Mabus said.

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Mabus and Defense Secretary Ashton B. Carter also have disagreed publicly about budgetary issues, with Mabus preparing a fiscal 2018 budget that includes billions of dollars in shipbuilding that Carter’s version of the budget does not support. In a memo released to the media this month, Mabus told Carter that he will not cut some ships from the budget at the expense of others.

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Mabus told Carter that “you and I both know that this budget is almost totally a symbolic one,” noting that President-elect Donald Trump will take office soon and have his own priorities. The Navy declined from 316 to 278 ships as a result of how few ships were put under contract between 2001 and 2008, Mabus wrote, calling it a lesson “that we should not have to learn twice.”