On the morning of January 20th, the day Donald Trump was inaugurated, in Washington, D.C., a large group of anti-Trump protesters, dressed in black, roamed through the city for close to an hour. Some chanted, some dragged newspaper boxes into the street, and some smashed the windows of various stores. In response, the police arrested more than two hundred people, setting in motion a complex legal saga that, months later, is far from over.

On Wednesday, the American Civil Liberties Union of the District of Columbia filed a federal lawsuit accusing the police of violating the rights of several people by using pepper spray and explosive devices without warning or justification; by making a mass arrest without differentiating between those who had broken laws and those who hadn’t; and by holding detainees for hours without food, water, or access to toilets, and subjecting some to “humiliating and unjustified” invasive searches.

The four plaintiffs in the A.C.L.U.’s lawsuit include Shay Horse, a twenty-three-year-old whose Twitter account identifies him as a photojournalist and “scrumptious/rambunctious anarchist.” According to the lawsuit, Horse broke no laws on the day of the protest but was doused with pepper spray, trapped between police lines for several hours, and then arrested and subjected to a rectal probe. In February, prosecutors dropped all charges against him. The other plaintiffs are Milo Gonzalez, a protester who, the lawsuit says, was also subjected to a rectal search after his arrest and was denied access to a bathroom for nine or ten hours; Elizabeth Lagesse, who, according to the suit, did not break any laws before being arrested but was handcuffed so tightly her wrists bled; and a lawyer named Judah Ariel, who said that he was among a group of people on a sidewalk who were pepper-sprayed without cause but not taken into custody.

The protest—which used tactics long associated with anarchists and anticapitalists, including dressing in black to create a sense of solidarity and to make it difficult to distinguish individuals—was the most confrontational to take place in Washington in more than a decade, and it provoked an unusual response from local prosecutors: they obtained indictments charging more than two hundred people with conspiracy and with instances of property damage that appear to have been carried out by only a few individuals.

The morning protest was broken up following a mass arrest that police conducted around 11 A.M. on L Street, but others continued for hours afterward, causing a significant disruption in the city. According to the authorities, protesters damaged more than a hundred thousand dollars’ worth of property in the course of the day. On K Street, some protesters threw rocks and set a limousine on fire. Police officers, wearing helmets and carrying plastic shields, tried to quell that crowd, and officials have said that several officers were injured in the clash, including one who was briefly knocked unconscious.

Dustin Sternbeck, a spokesman for the D.C. Metropolitan Police Department, said that the police do not believe that the protesters participated in “a First Amendment assembly.” Instead, he said, they had acted in “a concerted effort” to destroy property, using crowbars, hammers, and collapsible metal batons. “We stand by our assertion that officers acted responsibly and professionally during the riot and believe our officers made reasonable decisions during extremely volatile circumstances,” Sternbeck wrote recently, in an e-mail. In response to the A.C.L.U. lawsuit, he added, “All instances of use of force by officers and allegations of misconduct will be fully investigated.”

While it seemed clear on the day of the protest that the vandalism and property damage were committed by a small number of people, a superseding indictment handed down in late April charged two hundred and twelve people with rioting, inciting a riot, and engaging in a conspiracy to “damage, destroy, or deface property.” Because participants in a conspiracy can be held responsible for an offense committed by a co-conspirator, the defendants were all charged with breaking the windows of a Bank of America branch, a McDonald’s restaurant, a café, and two separate Starbucks stores. All of them faced the possibility of lengthy prison sentences.

According to defense lawyers, there appears to be no modern-day precedent for charging everyone arrested during a particular protest with conspiracy, and, in May, thirty of the accused filed a motion saying that those charges lacked merit and asking that the superseding indictment be dismissed. Lawyers from the Georgetown Criminal Justice Clinic, white-shoe firms like Arnold & Porter Kaye Scholer, and D.C.’s Public Defender Service joined in the motion, which argued that the indictment had attributed crimes “collectively and indiscriminately” to defendants without offering evidence of individual culpability.

Some of the defendants have said that they believe they are being targeted for their perceived political identity. Calls for an “anti-capitalist anti-fascist bloc” on Inauguration Day had begun circulating soon after the election in November. Social-media messages included a photograph of a group of black-clad figures brandishing flags and what appear to be flares along with the hashtag #disruptJ20 and the words “wear black.” A communiqué on the Web site CrimethInc read, “If Trump is to be inaugurated at all, let it happen behind closed doors, showing the true face of the security state Trump will preside over. It must be made clear to the whole world that the vast majority of people in the United States do not support his presidency or consent to his rule. . . . We must take to the streets and protest, blockade, disrupt, intervene, sit in, walk out, rise up, and make more noise and good trouble than the establishment can bear.”

The authorities seemed aware of the political leanings associated with the protest. Charging documents said that police officers had been “monitoring a planned assembly of individuals that were known to be associated with an anarchist group” and that intelligence-division officers knew that they would be gathering “with the express intent to disrupt Inauguration-related activities.”

Prosecutors in D.C. now face a potentially daunting number of cases, and whether they will be able to come up with individual evidence for each defendant’s case remains to be seen. So far, according to court documents, they have looked at photographs taken by police officers, reviewed video footage, and obtained a judge’s permission to search more than a hundred cell phones seized from those who were arrested. In March, they obtained a warrant to search the home of a man described as a protest organizer and to take computers, cell phones, tablets, and any material documenting the planning of a “riot or ‘Black Bloc’ march” or the planned destruction of property.

The A.C.L.U. suit doesn’t address decisions made by prosecutors in the past few months but it does call into question the police tactics that preceded the Inauguration Day arrests. Scott Michelman, the senior staff attorney for the A.C.L.U. who is handling the case, told me that he and his colleagues had been troubled by the events of January 20th, saying that officers had “forced a bunch of people into a mass detention whether or not they had any involvement in unlawful activities.” The suit, he said, was meant, in part, to send a message to the city that it should avoid “guilt by association policing,” which could threaten First Amendment rights, particularly during events of national political significance, when protests are bound to take place.

“When this sort of thing happens on Inauguration Day, it raises a special level of concern,” Michelman said. “People in the future will start thinking, Well do I want to go to this demonstration, or is there a chance somebody’s going to break a window and I’m going to end up getting charged with multiple felonies that could put me away for more than ten years?”