This post has been updated.

Just as students at Lincoln High School were filing in their seats Monday morning for the start of another school day, their principal, Esther Omogbehin, was sitting down with Superintendent Cindy Marten, mulling whether to walk away from Lincoln.

Between Omogbehin and district staff, one thing was clear: Something had to give.

On Tuesday, Omogbehin made the official call. She’ll bow out, and will be placed on paid administrative leave while the district decides her fate, said Superintendent Cindy Marten.

San Diego Unified will appoint John Ross, a vice principal at Mira Mesa High School, as interim principal until it finds a permanent replacement, Marten said.

Omogbehin, or “Dr. O.,” may be the most polarizing principal within San Diego Unified. In the two years she’s had control of the school, Lincoln has been a war-zone – torn between those who see her hard-lining approach as answer to sputtering test scores, and those who rabidly oppose her top-down leadership style.

Friday night, NBC 7 reported that school board Trustee Marne Foster asked Omogbehin to step down from her post.

Omogbehin says that none of that was true.

“It wasn’t in the context of asking me to leave. It was asking me, ‘Do you need a break?’” she said.

“Because of relentless pressure, (school board Trustee Marne Foster) asked me if I thought it would be best if I went on to a different path instead of having to interface with these weak teachers, these empty vessels that make the most noise and bully other people,” Omogbehin said.

Foster did not respond to a request for comment.

For decades this storied school had been the pride of the black community. But in 2003, when the school closed to rebuild its campus, its students were scattered. The community applauded when it opened the 2007 school year with a sparkling $129 million campus.

It opened with four separate academies: a center for social justice, arts, science and one for engineering and public safety.

Students returned in droves, but the school was never able to rebuild the same sense of community.

By 2012, Lincoln ranked last in the district in its Academic Performance Index, a number based on standardized test scores. The school was hemorrhaging students. Staff turnover was continuous.

That year, when Omogbehin took over, she promised to crack down on ineffective teachers.

The battle lines were drawn. Teachers complained that Omogbehin’s leadership style was unnecessarily abrasive and confrontational.

It made for a dysfunctional marriage from the start. Shortly after Omogbehin landed, a student accused her of physically threatening her after she stood up during an assembly and shouted that everybody hated her. Nothing ever came of the allegations, but it foreshadowed a deeper tension that exists today.

Omogbehin again stoked the fire when she pushed to restructure Lincoln’s campus, moving from four academic centers to a single-functioning complex, despite objections from teachers.

Toxic debates regularly spilled from Lincoln to the floor of school board meetings.

But Omogbehin wasn’t universally loathed. Those who supported her did so fervently. Members of the tight-knit black community, teachers who dug her style and school reform advocates had her back throughout her tenure.

The drama reached a fever pitch this past fall, when disgruntled teachers hit the streets and the school board in protest, calling for the principal’s removal.

In five years, Lincoln had gone from a crown jewel to one of San Diego Unified’s biggest stains. It’s expensive, it’s clunky, it’s ineffective – it’s a symbol of everything that’s wrong with a large urban school district.

A Complicated Legacy

It would be too simple to say Omogbehin hasn’t had made any positive impacts.

A revamped department helped boost student math scores last year, and while scores were still very low – only around 15 percent of ninth grades scored proficient in algebra – it represented marked improvement from previous years.

And after she ordered a transcript audit, Omogbehin found that out of 350 would-be seniors, only 50 were on track to graduate. Omogbehin said that by retooling students’ schedules, and having them double up on needed classes, she moved that number to about 325.

Still, the school remains in Program Improvement – a type of academic probation imposed by the feds for schools that fail to make progress.

This past winter, Foster rallied support for a plan to establish what’s called a middle college at Lincoln – where students earn college credit while in high school. It offered a sign of hope that the school could draw more students to its doors.

The idea was well-received, and talks to make it happen have been under way. Ironically, the very plan that could bring relief to Lincoln might have also set the stage for Omogbehin’s departure.

A district source who only agreed to speak confidentially said that Omogbehin liked the idea, but didn’t want to have to ask the union for waivers, a necessary step if Lincoln was going to have flexibility from the rules in more traditional schools.

During the conversation, Omogbehin told union representatives she didn’t care whether she had their support or not, and as a result, lost Foster as a supporter, the source said.

“Right then, (Foster) saw that for Dr. O., this had become more about herself than the kids,” the source said.