Mission Control Command Center – Another Attempt to Target Nonprofits –

The latest report that the FBI and IRS have created a new “mission control command center” to investigate nonprofits for possible ties to political violence or domestic terrorism should alarm the nonprofit sector. Not because nonprofits are above the law. They are not. But because this appears to be another step in a growing effort to use federal power against organizations whose work does not fit the administration’s political agenda.

Why This Matters

Many nonprofits work on issues that are politically charged. They organize communities. They support litigation. They speak out on public policy. They help people show up, advocate, and resist government overreach. They work on immigration, racial justice, reproductive rights, LGBTQ rights, voting rights, environmental justice, and religious freedom.

That work is often controversial. But controversy is not a crime. Much of this activity is protected by the First Amendment. That is exactly why it is so troubling to see the government use broad and loaded terms like “domestic terrorism” and “political violence” in ways that may pull lawful nonprofit work into the reach of federal investigation.

This Has Been Building for Months

This reported FBI and IRS initiative is not new. Last September, President Trump issued an executive order attempting to designate Antifa as a domestic terrorist organization. That move was legally and factually questionable from the start. Antifa is not a formal organization in any ordinary sense, and federal law does not provide the same kind of domestic terrorist designation system that exists for foreign groups.

Soon after that, the White House issued a national security memorandum laying out a broader strategy to investigate and disrupt people and groups tied to political violence and intimidation. The language in that memo was broad and ideological. It suggested that certain political beliefs and advocacy positions could be treated as signs of extremism.

Then, in December 2025, Attorney General Pam Bondi reportedly directed federal agencies to prioritize these matters and compile lists of groups, including nonprofits, that might fall within the administration’s new framework. Now the latest reporting suggests that the FBI and IRS are building on those earlier actions with a new joint operation focused on nonprofits.

The Problem Is Not Ordinary Law Enforcement

If a nonprofit or its leaders are actually engaged in criminal conduct, the government already has tools to investigate and prosecute that conduct. No one disputes that. The concern here is different.

The concern is that the government is building an enforcement structure that can be used to investigate nonprofits without clear evidence of wrongdoing, based instead on suspicion, ideology, association, or opposition to administration priorities.

That is where the danger lies. When law enforcement and tax enforcement are pointed at organizations engaged in lawful advocacy, the message travels quickly. It tells the sector that certain kinds of work may come with political risk, even if the work itself is legal.

The Chilling Effect Is Real

A nonprofit does not need to be charged with a crime to suffer harm. An investigation alone can be enough.

Donors may step back. Banks may ask more questions. Board members may become nervous. Fiscal sponsors may avoid projects that seem politically sensitive. Staff may narrow programs to reduce risk. Lawyers may advise caution in ways that slowly reshape what organizations are willing to do.

This is how civil society gets squeezed. Not always through direct bans or prosecutions, but through fear, uncertainty, and the rising cost of dissent.

What Nonprofits Should Do Now

This is not a moment for panic. But it is a moment for care. Nonprofits should make sure they are doing the basics well. They should keep strong records. They should maintain clear internal controls. They should review how advocacy, protest support, grantmaking, and public communications are structured. They should be thoughtful and disciplined about legal compliance.

That said, nonprofit leaders and their lawyers should not mistake this for a routine compliance issue. It is also a civil liberties issue.

If the government is using investigative tools to target organizations because of their viewpoint, their associations, or the causes they support, then the threat reaches far beyond any one nonprofit. It goes to the heart of free speech, free association, and the role of civil society in a democracy.

Why Everyone Should Care

This is bigger than any one administration and bigger than any one cause. A healthy nonprofit sector is part of what makes democracy work. Nonprofits give people a way to organize, speak, serve, and challenge power. They often represent communities that have little access to formal political institutions. They help create accountability when government fails.

When government power is used to intimidate nonprofits engaged in lawful work, the damage is not limited to the organizations under scrutiny. The damage spreads outward to donors, volunteers, communities, and the public itself.

That is why this development deserves close attention. The issue is not whether nonprofits should follow the law. Of course they should. The issue is whether the government is using the law, and the threat of enforcement, as a weapon against lawful dissent. That should concern all of us.

Ellis Carter is a nonprofit lawyer with Caritas Law Group, P.C. licensed to practice in Washington and Arizona. Ellis advises nonprofit and socially responsible businesses on federal tax and fundraising regulations nationwide. Ellis also advises donors concerning major gifts. To schedule a consultation with Ellis, call 602-456-0071 or email us through our contact form.