Richard Wolf

USA TODAY

Corrections and clarifications: An earlier version of this story misidentified the Alabama official leading efforts against same-sex marriage in the state. It is the state's chief justice.

WASHINGTON — When the Supreme Court declared a constitutional right to same-sex marriage last June, the man who won the leading case warned that opponents would find new ways to push back.

“We will have to continue the fight,” Jim Obergefell said then — and he was right.

For nearly a year, seesaw battles over religious exemptions and transgender rights have replaced what had been the gay rights movement's steady progress in winning protections against discrimination in states and cities. Legislative and legal skirmishes have been triggered by an intransigent Alabama chief justice and a defiant Kentucky county clerk, a Colorado baker and a Washington State florist, and most recently a conservative backlash that has traveled east from Texas to Mississippi to North Carolina.

"We never thought this had to do with just marriage," says Kristen Waggoner, senior vice president of legal advocacy at Alliance Defending Freedom, which represents many gay rights opponents in court. "This is about more than marriage.”

It's also about more than bathrooms, although a North Carolina law that denies transgender people the right to use public restrooms corresponding to their gender identity has dominated the LGBT rights debate for the past two months:

Some states, led by Mississippi and North Carolina, have enacted laws intended to protect those who deny services to gays, lesbians, bisexuals or transgender people because of religious objections. Tennessee and Kansas have passed less sweeping religious exemption laws.

Lawsuits stemming from individual merchants' refusal to participate in same-sex nuptials continue to move through state and federal courts. The most prominent cases involve a Colorado "cake artist," Washington state florist and wedding venues in Illinois and New York.

Across the country, the gay rights movement has been met with local opposition — sometimes where it was least expected, such as Houston, which had three times elected a lesbian mayor. That has forced the movement back on the defensive less than a year after its greatest success: the Supreme Court's 5-4 decision in Obergefell v. Hodges that extended same-sex marriage nationwide.

Supreme Court strikes down bans on same-sex marriage

“To some, this is the next front in the war," says David Stacy, government affairs director at the Human Rights Campaign, the nation's largest gay rights organization. “Some of the intensity on the other side, some of the emotional intensity, comes from that.”

Both sides in the battle say it's about individual rights — LGBT rights to live free from discrimination, and religious or moral rights to live free from government interference. It extends to education, employment and housing — and it may not be long before a lawsuit is headed back to the Supreme Court.

“I think this moment is going to be short-lived, but a lot of damage can be done in this moment," says Shannon Minter, legal director at the National Center for Lesbian Rights. “It will ultimately be up to the Supreme Court to decide whether Title VII (of the Civil Rights Act) and Title IX (of the Education Amendments Act) fully protect transgender people, and for that matter gay people."

Obergefell planted seeds

Justice Anthony Kennedy's historic ruling on same-sex marriage included a single paragraph warning of the war to come.

"The First Amendment ensures that religious organizations and persons are given proper protection as they seek to teach the principles that are so fulfilling and so central to their lives and faiths, and to their own deep aspirations to continue the family structure they have long revered," Kennedy conceded. "The same is true of those who oppose same-sex marriage for other reasons."

Those battles had begun long before the Supreme Court's decision. In states where same-sex marriage already was legal, merchants who refused to participate in gay and lesbian weddings based on religious objections were the targets of lawsuits. Most of them lost the early rounds and have appealed.

The first major sign of resistance after the high court's ruling came out of left field. Voters in Houston, where Mayor Annise Parker in 2010 became one of the first openly gay mayors of a major U.S. city, rejected a City Council-passed ordinance to protect residents based on characteristics that included sexual orientation and gender identity. The simple slogan: "No Men in Women's Bathrooms."

"They identified an opening and exploited it," says James Esseks, director of the American Civil Liberties Union's LGBT efforts.

Then this year, state legislatures in South Dakota, Georgia, Mississippi and North Carolina passed laws pushing back against LGBT rights. The bills were vetoed by Republican governors Dennis Daugaard in South Dakota and Nathan Deal in Georgia but signed by Mississippi's Phil Bryant and North Carolina's Pat McCrory.

Mississippi's law protects those who deny services based on religious objections to gay marriage or transgender people. North Carolina's prevents the state and its municipalities from establishing civil rights protections based on sexual orientation or gender identity.

"You're seeing an explosion of religious liberty legislation in the wake of Obergefell," says Mat Staver, chairman of Liberty Counsel, a conservative law firm and think tank involved in the effort. He calls it "just the tip of the iceberg of what we will see as Obergefell begins to settle on the rest of the country.”

The fight reached the floor of the House of Representatives this month over an amendment intended to ban federal contractors from firing workers who are gay, lesbian, bisexual or transgender. The measure was blocked, then passed, then blocked again.

Stalled in the states

Beset by such conflicts, gay rights advocates have made little progress in the past year on their major post-gay marriage agenda: passing state laws protecting the LGBT community against discrimination in employment, housing and public accommodations.

Utah was the 22nd state to pass such a law in March 2015. Since then, gay rights activists have met a wall of opposition in the remaining 28 states, mostly led by Republican governors and legislatures.

“People are using Obergefell now to say 'I can get married on a Sunday, but then I can go into work and get fired on the next day,” says Travis Weber, director of the center for religious liberty at the conservative Family Research Council.

Even so, he says, "There’s a need to protect religious dissenters.”

The two sets of legal skirmishes — over religious exemptions and transgender rights — "have made it difficult for us to move forward," Esseks says. He calls them "responses to the reality of the freedom to marry nationwide."

There have been some victories for LGBT rights. Last month, a federal appeals court in Richmond ruled in favor of a transgender boy's right to sue a Virginia school district over its bathroom policy. A handful of states, led by New York, have banned the use of controversial conversion therapy on minors.

“It’s not as though we’re not making any legislative progress. We are," Minter says. Even the prospect of passing non-discrimination laws in 'red' states, he says, "is actually much less daunting after Obergefell than it was before.”

But energized by their loss at the Supreme Court last June, religious objectors are fighting back amidst a presidential election that has divided the country along geographical, ideological and cultural lines.

"What’s at stake right now is so much bigger than whether someone has to shower with someone of the opposite sex,” Waggoner says. "I think Obergefell opened that door more broadly than it had been before. It not only jeopardizes religious freedom, but it jeopardizes all of our religious liberties.”