Here’s a fight we have never seen before: Americans from opposite ends of the political spectrum fighting over the separation of church and state, the size of government, God’s business in politics, and what it is OK to do, or not do, with our tax money.

The latest battle was waged by the Freedom From Religion Foundation (FFRF), a Wisconsin-based atheist group which sued the Internal Revenue Service (IRS) in December 2012 over its failure to police churches engaging in illegal “electioneering” — sometimes straight up telling parishioners who to vote or not vote for.

The group, which has been reporting churches illegally preaching politics for years, settled with the government agency July 17, after it became “satisfied” that the IRS would "resume doing its job." But that, of course, angered religious groups across the country, which have filed their own legal actions and accused the agency of signing “a secret pact with atheists.”

But while the FFRF hailed the settlement with the agency as a “victory,” the IRS is not about to start auditing “rogue” churches quite yet.

The government agency has recently come under fire after allegations that it has profiled conservative groups seeking tax exemptions, deliberately subjecting them to increased scrutiny. As a result, all of its audits, of churches or other groups, are currently on hold while a Justice Department investigation is under way.

'The religious right is all wrong as usual. We were suing the IRS, they are not in cahoots with us.'

“The main point of our lawsuit was to force the IRS to go back to enforcing its own law, we are satisfied that the IRS intends to do that,” Annie Laurie Gaylor, co-president of the FFRF told VICE News. “But of course what’s unsatisfactory right now is that everything’s on hold because of the congressional Tea Party probe. Nothing’s happening right now on any front with the IRS.”

But a number of churches and conservative groups are also trying to make sure that nothing happens with the IRS anytime soon.

In December 2013, a small Milwaukee-based church, Holy Cross Anglican Church, filed a motion to intervene in the FFRF suit, which was granted. Days after the FFRF and the IRS settled last month, however, the church filed and lost an opposition to the FFRF’s motion to dismiss its lawsuit “without prejudice” — meaning the group could restart the lawsuit if the IRS fails to act.

Also following the settlement, the Alliance Defending Freedom (ADF), a conservative Christian group, filed a Freedom of Information Act (FOIA) request for details of the IRS exchanges with the FFRF. The ADF did not respond to VICE News’ questions.

A spokesman for the IRS declined to comment on either the settlement itself or the FOIA request. But the group behind the lawsuit accused conservatives of unleashing an unfair “witch hunt” against the agency.

“The religious right is all wrong as usual, either they’re trying to say that our victory is a defeat or they are busy saying that we’re in cahoots with the IRS, which is just a fantasy,” Gaylor said. “We were suing the IRS, they are not in cahoots with us.”

'Father Malone believes that he has a duty to preach on the issue of the sanctity of human life and this can sometimes have political implications.'

Vicar Patrick Malone, the Holy Cross Anglican Church’s pastor named in the suit, did not respond to VICE News’ calls and emails, but the group was represented legally by the Becket Fund for Religious Liberty, a DC-based pro-religion group whose clients include Hobby Lobby.

“The FFRF was trying to force the IRS to censor churches’ speech and Father Malone and Holy Cross Anglican Church felt that they had a religious obligation to say the things that the FFRF wanted censored,” Daniel Blomberg, a legal counsel for the fund, told VICE News. “For instance, Father Malone believes that he has a duty to preach on the issue of the sanctity of human life and the need for his congregants to stand up for people who can’t speak for themselves, both the very, very young and the very old, and these issues can sometimes have political implications and direct political connections.”

But preaching on issues like abortion during elections, or even endorsing candidates, critics said, would essentially turn churches into PACs.

God, Government, and Taxes

The debate over the separation of church and state — and how it should affect public money in particular — is hardly a new one.

At the IRS, “it’s been going on probably for 75 years,” Marcus Owens, a lawyer specializing in tax exemption who spent 25 years at the agency, told VICE News. “Ever since the 1930s the government has been struggling with how to deal with tax-exempt organizations that are engaged in the public policy debate,” he said.

At the heart of the current debate is the Johnson Amendment, a 1954 change to US tax code which prohibits tax-exempt organizations — including religious institutions claiming such status — from endorsing or opposing political candidates.

Then-senator Lyndon Johnson reportedly pushed the amendment through Congress after a religious broadcaster spoke critically of him during a campaign. “Whether that’s true or folklore, who knows,” Owens said.

Unsurprisingly, pro-church groups really don’t like it.

“To the extent that it restricts what churches can say, and what a pastor can say to his congregation about issues of moral importance, the Johnson Amendment violates the constitution,” Blomberg said. "The bottom line is that whether you think that churches should be preaching about issues that have political implications or not, it should be the decision of religious leaders and houses of worship, and not the IRS and certainly not a militant atheist group.”

Blomberg suggested that the FFRF settled on the case because they realized “they would lose in court” and added that the IRS has tried to avoid cracking down on churches, limiting itself to “threatening them with enforcement” out of fear of a court confrontation.

'We would lose our democracy because churches would become political wards and tax money would be laundered into political money and there would be no accountability, and churches are already not accountable.'

But Owens, the former IRS guy, defended the agency.

“The Becket Fund have also studiously avoided litigation,” he said, adding that, “Congress revisited [the Johnson Amendment] on two occasions and strengthened it both times, and the courts have consistently upheld it, including challenges to its constitutionality.”

The Supreme Court itself has not ruled on the campaign prohibition itself — nor has it been asked to, so far. But the prospect of legalizing politicking in church is terrifying to many who would prefer less money in politics because, you guessed it, churches have a lot of money.

“If this was allowed to proceed it would make Citizens United look like child’s play,” Gaylor said, referring to the Supreme Court case that essentially gave corporations free rein to engage in political lobbying.

“We would lose our democracy, we really would, because churches would become political wards and tax money would be laundered into political money and there would be no accountability, and churches are already not accountable,” Gaylor added. “It’s really a very serious threat.”

Freedom to Preach?

The FFRF has filed 53 complaints to the IRS since 2006, and 28 in 2012 alone — a presidential election year. It filed this lawsuit against the IRS in 2012, following reports of widespread abuse of tax exemption during the presidential race.

“They were very egregious Pulpit Freedom Sunday type of violations, with the ministers getting up on the pulpit and explicitly telling people to vote for Mitt Romney,” she said.

Pulpit Freedom Sunday is an effort that was launched in 2008 by a number of pastors and the conservative Christian group ADF explicitly challenging the IRS requirement that tax-exempt organizations like churches abstain from endorsing candidates.

The initiative is popular in election years and the next nationwide event is scheduled for October 5.

'The IRS is an equal opportunity censor.'

Supporters have claimed that pulpit freedom days — just like preaching politics in church on any other day — are part of their religious right, which the IRS is trying to censor. "It's not a deliberate attempt to break the law at all, because the law is the First Amendment the constitution controls," said Blomberg. "When an agency passes regulation, that can’t override the constitution.”

But paying for a certain kind of speech is not the same as prohibition, Owens rebutted. In other words, pastors can preach all the politics they want, they just can’t do that while getting a tax break.

“The tax code doesn’t prohibit it, it simply says that if it’s conducted in a certain context it gets a different tax treatment,” Owens said. “If a charity does it, the charity no longer qualifies for exemption, it doesn’t mean the charity goes out of existence. If a church loses its tax-exempt status it doesn’t lose its ability to conduct religious services or, for that matter, accept charitable contributions.”

Some critics of the IRS and the FFRF have also accused them of singling out conservative churches, ignoring more liberal ones, and adding that “politicking” is also widespread in many black churches.

“Conservatives have suggested that... FFRF isn’t much concerned with such groups,” an op-ed in National Review pointed out.

“It’s all propaganda,” Gaylor said, in defense of the group.

“If the people who are breaking the law happen to be breaking the law because they are ultra-conservative, what can you do about it? You don’t see this with the Episcopalians... that’s not targeting ultra-conservatives, that’s the ultra-conservatives who are just happening to be breaking the law,” she added. “That’d be like saying somebody who’s speeding can't be arrested if they’re Republican because you’re then targeting Republicans. That’s not the way the law works.”

As an example, she described a 2012 complaint the FFRF filed to the IRS about a church in North Carolina, where the pastor was wearing a pro-Obama T-shirt during his sermons. The IRS has actually targeted liberal churches as well, Blomberg agreed, citing a 2004 case in which the agency went after a liberal pastor for “basically saying that Jesus would vote for John Kerry.”

“The IRS is an equal opportunity censor,” Blomberg continued. “But one of the problems with what the IRS is doing is that it allows whoever is in power to abuse the resources of the IRS to go after speech that they don’t like.”

But the IRS is about administration, not politics, said Owens, dismissing the recent Tea Party attacks against the agency that it accuses of targeting groups and individuals critical of the administration.

“There has never been any evidence of that after the Nixon administration,” Owens said, conceding however that as the IRS largely operates by responding to complaints, “those complaints might be politically motivated.”

He also dismissed criticism of “IRS law.”

“The terminology is important because a lot of less sophisticated noise talks about the ‘IRS overstepping, encroaching,'” he said. “The IRS is just administering a law that was passed by Congress. It’s not the IRS code or the IRS rule, it’s congressional law.”

Follow Alice Speri on Twitter: @alicesperi