Authorities hailed the indictment - with charges for beatings, threats from goon squads, and arson - as a bid "to change the culture of unions in Philadelphia."
Dougherty and the others have denied the accusations.
But in a city with an outsize reputation for labor-related violence and vandalism, prosecutions remain exceedingly rare, often stymied by hesitant victims, political pressures, and legal hurdles.
Pressed to recall the last large case against Philadelphia union members, federal authorities reached as far back as the 1980s to their case against Roofers Local 30-30B - a massive corruption probe that brought down 13 union leaders, three reputed mobsters, two lawyers, a judge, and a police officer on accusations of extortion, intimidation, and political bribery.
"These are very difficult cases to make," said Richard Scheff, the ex-federal prosecutor who handled the case. "It's difficult to find witnesses who will testify. For most, it's easier just to move forward and put it all behind you."
Although reports of labor-related violence in Philadelphia have declined over the last 40 years, the circumstances of the 2012 Quaker meetinghouse arson brought fresh attention to labor violence.
Vandals crept onto the project's muddy construction zone under cover of night four days before Christmas. The next morning, workers found the work site in disarray.
A burned-out shell was all that remained of their smoldering construction crane. Dozens of shaved-off bolts threatened the integrity of the structure's steel columns.
Reeves, the builder, estimated the damage at $500,000 and weeks of lost work.
Even so, he remained wary of cooperating with investigators, said George McClay, a former Philadelphia police lieutenant who handled the initial investigation.
Reeves "looked at me and said, 'How can I trust you? You're union, too,' " McClay, now Morrisville's chief of police, said. It took him a few moments to realize the builder was referring to his membership in the Fraternal Order of Police.
Reeves was eventually won over. But witness reluctance remained a problem for investigators.
Several developers contacted for this story declined to comment, saying they were wary of inflaming already tense relations with organized labor.
Fred Hagen, president of Hagen Construction in Bensalem, maintained he had never had a problem with the ironworkers union, despite an NLRB order issued just days before Tuesday's indictment that suggested simmering tensions between the two.
The decree barred Edward Sweeney, an ironworkers business agent charged in the federal case, from entering Hagen job sites or threatening employees with violence. Still, Hagen declined to elaborate on the circumstances behind the case.
"I have not personally had any negative experiences with the Ironworkers," he said in an e-mail.
Glenside contractor Steve Kane said he, too, was initially skeptical when police took on the case of an attack on two of his nonunion workers outside a King of Prussia construction site in 2010.
With fists and baseball bats, ironworkers shattered rear windows on his workers' trucks and chased fleeing men, indiscriminately throwing kicks and punches.
Two union members, caught on camera, eventually faced state assault charges. But both accepted plea deals that let them go with minimal jail time.
Upper Merion detectives said they suspected others in the attack, but a lack of cooperation hindered their efforts to build a case.
"I grew up in this city," Kane said. "When it comes to unions, you take care of your own business."
Investigators encountered similar hesitance in building their case against the roofers in the '80s.
"We had tape recordings of people being threatened and hit, and when we asked them about it, they would later deny it ever happened," said Scheff, the prosecutor.
Only by amassing hundreds of stories of fractured jaws and firebombed trucks that had gone unprosecuted for years did authorities eventually persuade witnesses to come forward.
By combining their tales, "there was a feeling that no one witness was going to be in this alone, that there would be enough strength in numbers to bring the truth forward," said LeRoy S. Zimmerman, Pennsylvania attorney general at the time.
Scheff cited another tool as key to assuring convictions - electronic surveillance.
With three microphones installed in the union's headquarters, FBI agents caught union head Stephen Traitz Jr. and others on tape counting out cash and stuffing money into envelopes destined for Philadelphia judges.
Court filings in the ironworkers case suggest prosecutors will again also rely heavily on recorded evidence.
The indictment quotes dozens of texts and conversations in which Dougherty, Sweeney, and other leaders allegedly congratulated one another for pulling off acts of vandalism.
"Nice hit," Sweeney texted the Quaker meetinghouse arsonists the day after the attack.
In another exchange, Dougherty allegedly vetoed a sabotage of a communications tower because it could put the union in the sights of the feds.
Later, indicted ironworkers business agent Francis Sean O'Donnell allegedly chastised a union member for creating a paper trail that could tie the ironworkers to an attempted arson by sending bills to the union for the acetylene and oxygen used in the attack.
Dougherty, who had authorized the action, agreed, saying: "He just got to be careful."
But even with such potentially damaging recordings, the ironworkers case could face hurdles that have plagued similar labor-violence cases.
Unions have repeatedly turned to a 1973 U.S. Supreme Court decision to fend off extortion prosecutions. USA v. Enmons barred lower courts from convicting union members under the anti-extortion Hobbs Act for violence tied to "legitimate union objectives," such as campaigning for raises or more union hires.
Lower courts have since differed on where to draw the line.
But federal prosecutors in Philadelphia have sought to avoid such land mines altogether, bringing their cases instead under racketeering laws.
That decision will require them to establish a pattern of behavior among multiple union members, instead of proving individual acts of extortion, said Robert Doren, a New York labor lawyer who often represents developers.
"They understand what arguments they are going to be facing, and it appears they have built their case around them," he said. "They've studied the cookbook on how to present this type of case."