Four days after Alex Pretti was fatally shot while filming officers taking part in the Trump administration’s immigration crackdown in Minnesota, the Homeland Security Department quietly opened an investigation at its office in St. Paul.

The target was not the Border Patrol agents who had killed Mr. Pretti, a 37-year-old government nurse, in late January. Instead, it was several left-leaning political organizations — labor unions, a climate change group, socialist collectives — that investigators believed had provided help and money to what they described as the “violent opportunists and agitators” on the street, according to newly released government documents.

As part of their inquiry, the documents show, homeland security officials used an array of invasive tactics during the first half of this year to gather information on many groups and individuals who were never accused of crimes, crossing the line that has traditionally stood between investigating criminal activity and political dissent.

In one instance, officials used administrative subpoenas to obtain more than three years of financial records from the Sunrise Movement, an environmental action group, and a labor union, the Communications Workers of America. That time frame went well beyond the civil unrest in Minnesota, which was prompted by the deployment of thousands of immigration agents to the state during the winter.

In another, investigators scrutinized three years’ worth of wire transfers made by the nation’s biggest health care workers union, the Service Employees International Union, in what they referred to as an inquiry into “domestic terrorist financing.”

The documents further detailed an expansive covert surveillance operation in which undercover agents spied on protesters and organizers at meetings held online, as well as in libraries, parks and churches, taking down not only what they said, but also their names and sometimes license plate numbers. The undercover agents also infiltrated group chats on Signal, listening as activists discussed coming demonstrations and their political opinions.

So far, none of the organizations targeted by the homeland security inquiry, conducted with the U.S. attorney’s office in Minnesota, have faced charges. And yet, as the investigation moved forward, prosecutors showed grand jurors a PowerPoint slide asserting that 18 groups — including the A.F.L.-C.I.O., the country’s largest federation of labor unions — were part of a conspiracy to impede the work of immigration officers in Minnesota.

Ultimately, that supposed conspiracy led in June to the indictment of 15 people accused of interfering with law enforcement agents as members of the far-left movement known as antifa.

By its own account, the institutional left in Minnesota, especially the labor movement, played a central role in bringing out hundreds of thousands of people to march in protest of President Trump’s immigration crackdown in the state. But the demonstrations — and corresponding efforts to monitor the movements of Immigration and Customs Enforcement agents — were largely undertaken by ordinary residents, most of whom have said they were committed to peaceful resistance.

“While federal agents repeatedly broke the law, ordinary people exercised their First Amendment rights to protect their neighbors,” said Aru Shiney-Ajay, the executive director of the Sunrise Movement. “The Trump administration is now trying to intimidate individuals and organizations who opposed his agenda.”

The Homeland Security Department did not respond to a message seeking comment. A spokesman for the U.S. attorney’s office in Minnesota declined to answer questions about the investigative tactics.

Some of the 15 people charged in the so-called antifa case did, in fact, belong to some of the unions and political organizations that faced scrutiny over several months during the spring and winter. But the newly released documents, which were disclosed as part of a motion asking for more details about the criminal inquiry, suggest that investigators used those tenuous connections to take a deep dive into the inner workings of the groups.

Kevin Riach, the lawyer who filed the motion, in Federal District Court in Minnesota, wrote that the homeland security investigation into the interference with federal agents “extended far beyond any potential threat to law enforcement safety.”

“It concluded, with no evidence (but obvious political animus),” he wrote, “that numerous Twin Cities unions and nonprofit organizations were involved in a widespread conspiracy,” adding that “it surveilled and surreptitiously gathered financial records generated by these organizations despite the lack of any connection between those organizations and criminal conduct.”

The investigation in some ways called to mind Cointelpro, the intrusive counterintelligence program that the F.B.I. ran against leftist groups from the 1950s to the 1970s under the leadership of the bureau’s director, J. Edgar Hoover.

The Minnesota surveillance reports in particular documented what largely appeared to be political activity protected by the First Amendment. They showed how undercover agents embedded themselves in a “noise protest” outside a hotel where immigration agents were staying and took down notes at other gatherings as demonstrators brainstormed ideas on how to protest the surge of officers who descended on Minnesota late last year.

Former federal prosecutors questioned why homeland security officials took the lead in a case that would typically be overseen by the F.B.I. Others said that the broad use of subpoenas targeting labor unions and other groups was unusual and concerning, especially if it turns out there was no evidence that the organizations were breaking the law.

“The government’s power to investigate is extraordinary, and with that power comes a responsibility to exercise care and restraint,” said Harry Jacobs, who resigned as the chief of the criminal division at the U.S. attorney’s office in Minnesota in January in protest over the Trump administration’s handling of the killing of Renee Good.

“An investigation should begin with a legitimate basis to suspect criminal conduct, not with a chosen institution or group,” Mr. Jacobs added. “Prosecutors must follow the facts and the law wherever they lead, rather than select a target and work backwards to build a case.”

Several of the groups that were targeted in the inquiry, known as Operation Puppet Master, and in a follow-up investigation called Project Whipple Shield, declined to comment. (Whipple Shield is a reference to the Whipple Building, which served as a hub of the immigration operation.)

When Daniel N. Rosen, the top federal prosecutor in Minnesota, announced the indictment of the 15 purported antifa members two months ago, he chose his words carefully, insisting that the defendants had been charged only because each of them had “violently opposed” federal agents taking part in the Trump administration’s immigration agenda.

“Be assured,” he told reporters, “the Department of Justice and my U.S. attorney’s office has and will distinguish between lawful protest and criminal conduct.”

But what Mr. Rosen did not disclose that day was that the charges filed against the 15 defendants stemmed from a sprawling investigation. Its tentacles had touched the lives of scores of ordinary people — teachers, veterans, union members — who in many instances had gotten together to do little more than discuss monitoring ICE agents or abolishing ICE altogether.

The case in St. Paul, like others against ICE protesters, arose from a sweeping directive issued last year by Mr. Trump known as National Security Presidential Memo 7. The memo ordered a whole-of-government approach to stem what officials have described as a rising tide of left-wing political violence.

But former prosecutors and civil rights lawyers have criticized it for encouraging aggressive investigations and prosecutions of groups and people on the left for activities typically protected by free speech laws.

In drafting their indictment, prosecutors under Mr. Rosen focused on an organization called Direct Action Minnesota, or DAMN, an umbrella group that describes itself as a “decentralized coalition of working-class people engaged in various forms of community defense against the current federal occupation” in Minnesota. Prosecutors said that the group trained its members in how to use shields against law enforcement officers, conduct surveillance, plan events and mount “rapid mass mobilization” against actions by ICE officers.

The indictment details some behavior by protesters with ties to DAMN that clearly seems violent or obstructive.

For example, prosecutors said that on Jan. 23, demonstrators who had gathered at the Whipple Building threw ice blocks at law enforcement vehicles. They also formed a blockade, boxing federal agents into one area near the federal building. Weeks later, prosecutors added, some of the defendants put debris in a road outside the building, trying to block access to it.

But the indictment also notes that the defendants often relied on information gleaned from group chats whose members tracked and monitored vehicles going to and from the Whipple Building — behavior that is not necessarily illegal. Indeed, the federal judge overseeing the case, Katherine M. Menendez, has already issued an order in a separate civil proceeding saying that protesters cannot be arrested simply for following federal agents in their vehicles.

Nonetheless, some groups that organized and ran the group chats were targeted by the surveillance operation and later identified in the prosecutors’ grand jury presentation as being part of the conspiracy to interfere with ICE agents. Other members of the alleged conspiracy were said to include the local chapters of the S.E.I.U. and the Democratic Socialists of America, a state teachers’ union — and even the Grease Pit, a small bike shop in Minneapolis.

In his motion, Mr. Riach described how federal agents took down the license plate numbers of people who attended a protest at a church in Roseville, Minn., and used that information to obtain their names. The agents then searched social media for images of the people, compiling an “intel work-up” that included detailed personal information about them.

“None of these individuals did anything other than engage in protected First Amendment speech in a church meeting room,” Mr. Riach wrote. “Yet now their personal information is memorialized in a D.H.S. dossier.”