By all accounts strong-willed and demanding, but also admired by many of the women she trained and led, Lt. Col. Kate Germano had an aggressive drive for parity that brought her into conflict with her male commander, as well as some of her subordinates.

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ALEXANDRIA, Va. — When Lt. Col. Kate Germano took command of the Marine Corps’ all-women boot camp, the failure rate of female recruits at the rifle range was about three times higher than that of their male counterparts, and there was no plan to try to improve it. “The thinking was, girls can’t shoot, so why bother,” she said.

So she worked with trainers to give women better skills instruction and soon passing rates soared, according to Marine Corps records. In June, 95 percent of women passed initial rifle qualification, equaling the rate for men.

Germano made similar gains in strength tests and retention — though scores on written tests went down — and advocated for better training for female recruits.

But if they liked her results, her commanders apparently did not like her style. By all accounts strong-willed and demanding, but also admired by many of the women she trained and led, Germano had an aggressive drive for parity that brought her into conflict with her male commander, as well as some of her subordinates.

After two internal investigations, Brig. Gen. Terry Williams, commander of Parris Island, the South Carolina home of the corps’ East Coast training operation, removed her from command June 30, saying he had lost “trust and confidence” in her ability to lead.

The corps said her removal had nothing to do with gender, and that an investigation had found that she disobeyed her chain of command and berated and embarrassed subordinates when they did not meet her standards.

“This whole thing started when her Marines — her female Marines — were telling us they were being mistreated,” said Col. Jeffrey Fultz, the chief of staff for Parris Island. “She was telling them their male counterparts will never respect them if they don’t get good physical scores. You just don’t do that.”

The episode comes at a critical moment for the Defense Department, which has mandated that the armed services integrate women into all combat roles by 2016, or provide clear evidence for why they cannot.

To many advocates of full gender integration, Germano’s dismissal has raised questions about the willingness of the Marine Corps, the most male-dominated of the services, to open the door to women in leadership roles. Why, those advocates ask, should a service that reveres its tradition of tough and demanding male commanders have problems with one who is a woman?

Germano, who had already put in her retirement papers before she was relieved of duty, declined to discuss why she had been fired. But in a request for relief she filed with the Marine Corps in May, she said the commander of the training regiment, Col. Daniel Haas, had created a toxic work environment and “consistently undermined my ability to command.”

A corps spokesman said Haas was not available for comment.

With its history and ethos built on the foundations of the male-only infantry, the Marine Corps is widely viewed as the most resistant of the services to full gender integration. It not only has the smallest proportion of women of all the services — 7 percent, compared with 14 percent in the Army and 15 percent in the Navy — but also the highest rate of sexual assault, with 8 percent of female Marines reporting being sexually assaulted in 2014, according to the Defense Department.

“Out of all of the military, the Marines have struggled the most with integration issues,” said Greg Jacob, a former Marine infantry officer who is now policy director with the Service Women’s Action Network, a nonprofit group that advocates gender integration. “They have this archaic system that segregates women in boot camp, and the stigma that creates at the start of every Marine’s career really carries over.”

At her first ceremony as commander to mark the end of a training cycle, Germano noticed a row of chairs behind the women’s formation and asked what they were for. She said she had been told that they were for women who were too tired or sore to stand for the ceremony — which came at the end of a 9-mile march. The men did not have a row of chairs. She watched some women break formation and sit down.

“After that I ordered that the chairs be taken away,” she said. “That could be seen as me being mean, but the chairs sent a message to everyone that less was expected of females.”

Germano increased physical training. Soon the number of women completing the final march increased, she said. And everyone stood at the end.

Germano got the hike added at the end of each training cycle and tried to integrate other practice hikes, but some male commanders refused.

Germano said her relationship with the commander of the training regiment, Haas, had started to go bad soon after she arrived.

She began contacting recruiting stations to detail why some recruits had failed basic training — information she thought would help prevent failures in the future.

According to her statement, included in a command investigation obtained under the Freedom of Information Act, Haas told her to stop contacting recruiters, saying she was being overly aggressive. She responded that he would not say she was “being overly aggressive if I were a male.”

The male battalions had five drill sergeants for each group of recruits, but the female battalions had only three. Germano pushed for more staff, saying her sergeants were exhausted.

When Haas was not responsive, the investigation found, she went up the chain of command to request more staff, further straining their relationship and causing him to challenge all her command decisions.

“He has held a long-standing grudge against me for disagreeing with him,” she said in her request for relief. “And is now looking for any reason to discredit me.”

Haas told investigators their relationship “went south,” saying she disagreed with him over too many things, and went over his head a number of times. “Making an argument is OK and encouraged; being argumentative is not,” he said.