WILLIAMS, Ala. — In early 2017, a pastor in the Alabama countryside named Chris Thomas prepared to give his Sunday sermon. President Trump had been inaugurated the week before, and the new administration was already making headlines with a travel ban that included refugees from Syria.

Mr. Thomas knew of no one in his congregation who had ever met a Syrian refugee. Still, the ban deeply bothered him. So did the prospect of speaking against it from the pulpit, which he preferred to keep clean of politics.

And so that morning at First Baptist Church of Williams, a relatively liberal church with a mostly white congregation, he carried with him a sermon on the Beatitudes, eight blessings for the needy Jesus is said to have given to his followers on a hillside in Galilee.

“Blessed are those who mourn, for they will be comforted,” went one.

“Blessed are the meek, for they will inherit the earth,” went another.

To these, the pastor added a verse of his own: “Blessed are those who seek refuge and have the door shut on their face.”

What Mr. Thomas, a 35-year-old preacher with cropped sandy hair and a trimmed beard, didn’t know was the degree to which Mr. Trump’s election had already polarized his small church. Nor did he know how the Trump presidency would continue to fracture the congregation for the next three years — a rift which would widen and threaten his own stewardship of Williams Church as the culture wars spilled into its pews in ways he could not control.

A few days after the sermon on the Beatitudes, a group of congregants wanted to talk.

“They more-or-less said, ‘Those are nice, but we don’t have to live by them,’” Mr. Thomas recalls church members saying about the verses, a cornerstone of Christian scripture. “It was like: ‘You’re criticizing our president. You’re clearly doing this.’ From thereon, my words were being measured.”

Mr. Trump rose to power with a boost from evangelical Christians, and their role in his re-election bid has not been lost on the president this year. As governors restricted public gatherings to stop the spread of the coronavirus, Mr. Trump declared churches “essential” and threatened to override officials who prevented them from opening their doors.

He had protesters forcefully removed for a photo op with a Bible in front of a church amid demonstrations against police brutality. And this past week he attacked the Supreme Court after a ruling on protections for gay and transgender workers that was unpopular among some evangelical leaders.

The doors of Williams Church in Alabama are about 700 miles from Washington. But a conflict born of the Trump Era smoldered there for years.

After the sermon on the refugees, churchgoers began to monitor Mr. Thomas’ posts on Facebook, reporting back to each other when something the pastor “liked” was seen by them as too liberal. When a group of church missionaries returned from a humanitarian trip to the Mexican border, they got a cold welcome from those who said they supported Mr. Trump’s border wall plans. One family proposed a “watchdog” group to ensure new members weren’t gay.

Then in 2018, a small group of churchgoers led a secret attempt to oust Mr. Thomas to clear the way for a more conservative preacher.

“There’s no doubt the country is more polarized, and the church started to reflect it,” said Bobby Burns, a former member of the church’s finance committee. “The walls of this church just weren’t thick enough to protect us from the world.”

As America prepares for another presidential election, this time under extraordinary circumstances, the country church is taking stock of the toll the last few years have wrought: At least 40 congregants, a third of the congregation, have left Williams Church, many to pray at a rival church down the street that is more conservative. And this month Mr. Thomas announced he, too, would depart the church leaving Williams now without a pastor.

Wayne Flynt, a minister who is also a historian of Alabama’s Baptist churches, said they are hardly alone in their polarized pews, with Episcopal and Methodist churches throughout America caught in the same struggles. Two years ago the church he attends in Auburn, Ala., was voted out of the local church association after a dispute over gay marriage.

“This isn’t just about Christianity,” said Mr. Flynt, who grew up in Anniston, not far from Williams Church. “It’s about American culture and American politics in 2020.”

He thought for a moment and added: “That’s what you have at Williams Church. And it’s amazingly painful for a pastor to see that.”

Churchgoer and Pastor

Jim Green grew up in what might have been a typical conservative community in Alabama. His church, First Baptist Williams, was where he met his late wife Sally when they were children in the pews. The church sat at an intersection of two country roads alongside the only other gathering point in town, the general store. Beyond were the scattered homes of three families that had planted cotton after the Civil War — like him, all named Green.

But Williams was different, Mr. Green said. Alabama’s Jacksonville State University, where he worked, sat a short drive down the road, and many educators came to pray at the rural church. Rev. Barry Howard, one of Mr. Green’s ministers in the 1990s, recalled bumping into a group of men who drank coffee on old church pews that someone had put outside the general store.

“I would marvel at the retired professors and retired farmers there, and you didn’t know which was which,” he said. “They were carrying on conversations about philosophy, debating between Plato and Aristotle.”

Earlier that decade, the Southern Baptist Convention, the body that acted as a kind of mother church for the region’s congregations, had undergone an upheaval known as the “fundamentalist takeover.” A group of conservative pastors who believed the church had become too liberal began a purge.

In 1991, a small but vocal group of moderates split from the group and named themselves the Cooperative Baptist Fellowship. They pushed for more liberal theology, and, most contentiously among Baptists, to allow women to serve as pastors. Churches across the South were soon forced to pick which side to follow.

Even before the Baptists split, Mr. Green said, the conservative movement gave those at Williams some pause. The church’s choir director was thought to be gay and few wished to take a hard-line stance against one of their own. Mr. Green, who sat on the church leadership, said he wanted women to have equal roles to men.

He and other members pushed to nominate female deacons. Soon afterward, the church was expelled from the local Baptist organization.

“The fundamental churches around us said, ‘Oh no, you can’t do that,’” Mr. Green said. “We were voted out by some fine Christian people.”

On the other side of Alabama, the man who would come to lead the Williams Church was still a small boy growing up in the town of Enterprise, a short drive from the Florida border.

At his grandmother’s urging, his family attended a local church. But Mr. Thomas’ father was in his second marriage, and after he divorced again, the family’s welcome at the church ended, Mr. Thomas said. “The church was like, ‘You’re probably better off if you’re not here,’” he recalled.

The rejection weighed on Mr. Thomas but he eventually found his way back into the pews as a staunch conservative. Before his high school graduation, he had his class ring — which he no longer uses — engraved with two Confederate flags.

But academic life at seminary in Texas changed his views, exposing him to debates he’d never encountered in Enterprise. He learned of the differing views on women in the church, and about Gene Robinson, the Kentucky clergyman who became the first openly gay bishop of the Episcopal Church.

“These were the things my Sunday school teacher had never told me,” he said.

By the time he was on the job market, Mr. Thomas could see his politics had changed and told his wife, Sallie, that it might make sense for them to move to the East Coast where there were liberal Baptist churches. But as a Southerner, he had few connections outside of his home state, and the only church that hired him was back in Alabama.

From the start, it wasn’t a good fit. The racial tensions Mr. Thomas wanted to leave behind seemed always to be simmering there.

On a hot summer day Mr. Thomas was in his office when several African-American children were playing basketball outside, he said. One of them came to ask to use the drinking fountain in the church and Mr. Thomas pointed the child toward the door where the water was.

When a congregant, who was white, saw the black child approaching, Mr. Thomas said he pulled the door shut to not to allow the boy inside. The pastor was upset — it wasn’t the first time he’d seen that behavior.

“It was around that time I said, ‘OK, I need to get the old résumé written up again,’” he said, and decided to leave Alabama for good.

Mr. Thomas had recently published an article in the local newspaper about “11 a.m. Sunday Is Our Most Segregated Hour,” the Rev. Dr. Martin Luther King Jr.’s 1964 essay calling for the integration of Baptist churches in the South. The column had caught the attention of members of the committee that was searching for a new pastor at Williams Church. They called him for an interview.

Williams was different from the church and town he was trying to leave, they said. It had a mix of educators and farmers. It cherished tolerance in Alabama. And after the Baptist conservative resurgence, its members had sided with the church moderates.

When Mr. Thomas agreed to stay and be pastor at Williams, Wendell McGinnis, a member of the search committee said he saw a transformational figure in the offing.

“I said, ‘He will be unlike any other pastor we’ve ever had at Williams,” Mr. McGinnis said. “This wasn’t my opinion or anything, it was the spirit of Christ within me.”

At the Pulpit in Williams

The first major test came in the form of a note left in the church cemetery. It was signed by a group calling itself the local chapter of the Ku Klux Klan and the authors had left other copies around town, which was nearly entirely white, with vague vows to protect the community.

The note enraged Mr. Thomas, who had just started his tenure. Klan members had desecrated the graveyard where nearly every family in the church had relatives.

Mr. Thomas brought the note to the pulpit on the next Sunday morning and held it up.

“Christ doesn’t tolerate this, and we don’t tolerate this,” Mr. Thomas recalls saying. The congregation agreed.

Among those impressed by the new pastor was Jim Green. Now approaching his 80s, Mr. Green still lived in the same home he’d grown up in and could name pastors going back to World War II. He liked that Mr. Thomas was young. Mr. Green supported the vote to elect women deacons in the 1980s when an older generation of Baptists was still skeptical.

But the 2010s were shaping up to be a different time, Mr. Green said, and now it was the country’s progressives that seemed to be going too far. While he had once prayed alongside the church’s gay choir director, the legalization of same-sex marriage unnerved him. The undocumented immigrant population left him wondering if there would be resources remaining for his grandchildren’s generation.

And a figure outside the church began to draw his attention, Donald Trump. Mr. Green said Mr. Trump seemed brash but was highlighting key issues at a time where “we do not speak the truth.”

Mr. Thomas charged ahead into his new church. He gave sermons on Clarence Jordan, a Civil Rights-era Baptist who translated the New Testament in a Southern dialect to cast light on racial disparities, replacing phrases like “Jew and Gentile” with “white man and Negro,” and referring to Jesus’ crucifixion as a “lynching.”

It was a bridge too far, said Martha Almaroad. “We didn’t like the doctrine, we didn’t like what was being preached,” she said.

Then came Mr. Thomas’ speech on the Beatitudes and its indirect reference to Syrian refugees in the days after Mr. Trump’s inauguration.

“During the election and the time after, I think there was a solidification, or a coming out of some ways of people — all of a sudden you had people you would never imagine saying the things they say or doing the things they do,” the pastor recalled.

After some congregants met with Mr. Thomas in his office to voice complaints, others began to call him by phone. The criticism came from a minority and often implied that Mr. Thomas had a political bias. When Mr. Thomas gave a sermon asking what Jesus might post on a Twitter account, several congregants saw it as criticism of Mr. Trump and told him to stop the attacks.

Entire topics suddenly appeared off limits on Sunday: gay rights, immigration, anything to do with references to a wall. But the Bible is filled with stories about walls, Mr. Thomas said, from the Battle of Jericho where Joshua brings down the city’s walls with trumpets to the Israelites rebuilding the ramparts around Jerusalem.

“Now I was going over my sermon manuscript and thinking: ‘How is this sentence going to be heard? How is this phrase going to be heard?’” he said.

A liberal wing was starting to form within the church, often led by a retired businessman named Jim Justice. At 87 years old, Mr. Justice was becoming a progressive counterpart to Jim Green, the conservative church elder. He and his wife used to belong to a church in another town, but left in 2004 after it was taken over by a fundamentalist faction, he said.

“People in the pews never spoke up, they just sat there like lambs,” Mr. Justice said. He was determined that this wouldn’t happen at Williams.

Nor was Mr. Justice afraid to take his politics to church. In 2017, he joined Doug Jones’ Senate campaign in the county and asked churchgoers for permission to put up Democratic Party signs on their lawns. Mr. Green said no. Mr. Justice got a bumper sticker reading “I’m a Christian AND a Democrat.”

Williams Church wasn’t the only Baptist congregation in the South struggling with mounting polarization, and the following year, the Cooperative Baptist Fellowship, the moderate group created in the 1990s, started a task force to find common ground. One item on the agenda, well before the Supreme Court’s recent ruling that employees cannot be fired for their sexuality, was to update the group’s hiring practices regarding the L.G.B.T.Q. community. “It was like kicking off the top of an anthill,” Mr. Thomas recalled.

Mr. Green was one of the first to learn of the proposed changes, which would allow gay people to be hired for clerical positions within the fellowship, though not at local churches. He felt the changes were yet another attempt by leaders to be “politically correct.”

“He was on social media,” said Mr. Thomas. “I said ‘Jim, there’s nothing to worry about. I met with the people, I’ve got it printed out.’”

Mr. Green decided to circulate a petition to allow churchgoers to request their donations not go to the Baptist fellowship because of its policy to allow gay workers.

The petition was kept secret from the pastor. Peggy Reed Green, the church secretary, said a small group of petitioners would approach people after services saying the church was being led in the wrong direction. She wouldn’t sign.

“Sometimes that’s the way things are, you got a little group,” she said. “Because Satan’s everywhere. Satan is standing right outside of the doors when you walk out of church.”

Mr. Green’s position — along with other congregants he spoke to — now seemed to go beyond hiring policies and hardened into a stance on who would be allowed to pray.

“We wouldn’t accept an alcoholic as a deacon in our church,” Mr. Green said. “We wouldn’t accept a gay person into our church for the same reason, because they’re contrary to what our doctrines are.”

Churchgoers now realized a conflict was afoot between two growing factions. They called a meeting in a country wedding hall built in the style of a log cabin on the outskirts of the community. Both the conservatives and liberals each brought about a dozen people.

Wendell McGinnis, the search committee member who had pushed to hire Mr. Thomas, said he felt uneasy about the meeting from the start.

“I remember pulling up and I was thinking to myself ‘Wendell, you should just drive off,’” he said. “But I stopped the car and went in.”

The conservative faction aired their concerns. The church had become too liberal, they said. The congregation needed to take a firm stance against homosexuality.

“Finally I said, ‘What does someone propose the answer to all this is?’” Mr. McGinnis said, gesturing to the conservatives. “Then they said, ‘Well, maybe the solution is if Chris left. Then all would be well.’”

The liberals were shocked. Mr. McGinnis said he was heartbroken. He’d come to see the pastor “as close to a brother to me as I’ll ever have in this world.”

Still, the two dozen or so congregants decided the only solution would be to take the petition on funding — and any demands for Mr. Thomas to leave — to the church leadership and the pastor himself.

The meeting was called one afternoon at the church. The two factions agreed to sit outside at a group of picnic benches while representatives of each side met with the pastor in the church offices.

“I listened, I read the petition, and I sort of tried to calm the anxiety,” Mr. Thomas said. “None of our deacons had signed it. None of our staff had signed it.”

Someone said people had been tricked into signing. Anger began to rise within the congregation at what looked to some like a hostile takeover. The conservatives seemed to be losing.

And so when the tension finally burst into the open, the rage was not directed at the pastor. It was aimed at Mr. Green and his petition.

One of the congregants barged out of the room toward the picnic tables and pointed a finger at Mr. Green who was sitting with two dozen others, Mr. Justice recalled.

“He yelled at him and said: ‘Jimmy Green, you’ve been making trouble at this church for 40 years,’” Mr. Justice said. “You need to get out!”

Mr. Green, who declined to comment on what happened, was shaken according to those there. He said there had been a misunderstanding. The anger began to subside. But the damage was done.

“People may say things they regret for the rest of their life and wish they never said,” said Mr. McGinnis. “I think that was one of those things.”

An Exodus

In March 2018, six tornadoes descended from the skies in Alabama. One of them passed through the town of Williams, destroying a chapel there called West Point Baptist Church.

West Point’s minister, Ronny Moore, had a conservative style that stood in stark contrast to Mr. Thomas. He said he prayed for Mr. Trump and other leaders “constantly” on Sundays and during election season “tried to take the political side of things and bring it back to the biblical.” On L.G.B.T.Q. issues, he echoed Jim Green, saying being gay was a sin and the church should speak out against it.

And like it or not, Mr. Moore was presented with an opportunity to rebuild his congregation from the dissension at neighboring Williams Church.

One of the first to leave was Martha Almaroad, the congregant who took issue with Mr. Thomas’ early sermons. Jim Green’s daughter-in-law, Heather Dempsey left, along with her husband Chris, who had been part of the church leadership but troubled some for playing a Confederate in Civil War re-enactments.

Mr. Moore welcomed them all.

“I don’t know where your relationship with your church is,” he recalled saying to new arrivals. “But here’s my offer: While you’re between churches, until you find your church home, if you need a pastor, I would be honored.”

Yet for all the departures to West Point, roughly 40 people in all, Mr. Green was not among them.

“I was born into that church,” Mr. Green said. “I can tell you right here before God that everything I’ve done is to try to make things work, but I’ve been very much misunderstood.”

Mr. Flynt, the Baptist historian at Auburn University, said the departures from Williams “were the natural process of winnowing that takes place in a polarized society.” It would ultimately make the place more stable, he said.

This month, after weeks where the church stood mostly empty because of the coronavirus, Mr. Thomas prepared to open First Baptist Williams again. Yet there was one more departure that would be announced. It was his own.

Mr. Thomas quoted from the Book of Ecclesiastes, explaining that it was time to move on: “To everything there is a season, and a time to every purpose under the heavens,” he wrote to the congregation.

“Williams is like home for me, it’s very much like the place I grew up — I know the people, I speak the language,” he said in an interview afterward. But the last two years had shown the significant differences, too.

Racism had driven Mr. Thomas from his first church in Alabama; at Williams it had been gay rights that had caused the division.

He thought about Mr. Green.

“For the culture to have shifted under his feet without his permission was something that confused him,” he said. “He’s a man with a good heart.”

And he thought about himself and being a Christian at a turbulent time.

“I go between taking prophetic action — say what you need to say from the pulpit, take the consequences, it may be only half or a third join you — and thinking sometimes we’re all exhausted of it,” he said. “And maybe the church should be an oasis in the middle of this exhaustion.”