Police Commissioner Kelly views the NYPD's handling of the 2004 Republican National Convention as "one of the department's finest hours." So he said in a terse note to the Civilian Complaint Review Board that took issue with a May 2006 letter the board wrote Kelly—and sent to The New York Times—suggesting that police commanders might have been hasty in arresting hundreds of people at two demonstrations.

"As you well know, the convention served as a magnet for groups publicly committed to its disruption and to the disruption of life and commerce throughout the city," Kelly wrote. "Further, the convention brought with it the very real risk of a major terrorist attack…. Nevertheless, the convention, an essential element of American democracy, was able to proceed unhindered, while hundreds of thousands of others were able to dissent freely and openly."

During the week of the convention, the NYPD arrested more than 1,800 people for protesting—more than 1,100 of them on Tuesday, August 31, alone. As a whole, the arrests were the most seen at a U.S. protest in decades. Seattle police made around 500 arrests during the disturbances at the 1999 World Trade Organization summit there. At the 1968 Democratic National Convention in Chicago, around 700 people were arrested—but the police there might have been more interested in using their nightsticks than their handcuffs. Police at the 2004 RNC didn't crack skulls. But they hauled off a lot of people who apparently didn't belong in jail: Ultimately, only about 10 percent were found guilty of breaking the law. Whether or not the convention was the NYPD's finest hour, it was surely one of several hours during which the Bloomberg administration clashed with people seeking to exercise their freedoms of assembly and expression.

When the World Economic forum came to New York just a few weeks after Bloomberg and Kelly took power, the city expected to see a disruptive element that had already clashed with police in places like Seattle and Genoa. After all, the banks in town weren't taking any chances: They hired Beau Dietl & Associates, the private security firm, to protect their assets. Running BDA's show at the WEF was John Timoney, a former NYPD first deputy commissioner whose handling of the 2000 Republican National Convention in Philadelphia, where Timoney was then chief, involved "excessively harsh treatment" of protesters, according to Human Rights Watch. For their part, Kelly and the NYPD promised a zero tolerance approach to protesters who got out of hand.

The anticipated clashes didn't happen. Protest groups claimed that the "direct action" people—the folks who seek confrontation with the police—had simply skipped the event. The NYPD credited its own policies. "The amount of confrontation and the number of arrests were lower than expected," read one after-action report, heavily redacted for release as part of a lawsuit. "The staging of large amounts of personnel and equipment that was observed by protesters was a deterrent." The same report recommended in the future that police commanders at demonstrations "utilize undercover officers to distribute misinformation within the crowds."

In the late 1990s, New York began taking a tougher line on protests, veteran activists say. The NYPD stood out for the sheer number of helmets it assigned to demonstrations. What changed after September 11 was the way the NYPD cited the threat of terrorism as a rationale for how it handled protests—and political activity in general. Pointing to the threat of terrorists masquerading as a political movement, Kelly asked a federal court in 2002 to relax the restrictions under the Handschu consent decree, which had itself grown out of a 1971 lawsuit claiming that the police department illegally spied on and infiltrated political groups. District Judge Charles Haight agreed in early 2003.

Just weeks later, the city cited the threat of terrorism in blocking plans for an anti-war march past the United Nations on Saturday, February 15—just a few weeks before the United States invaded Iraq. The organizers had to settle for a stationary rally. According to the New York Civil Liberties Union, the police refused permission for the march after Kelly met with Bloomberg about the organizers' request. The organizers sued, the Justice Department jumped in on the city's side, and the judges sided with Bloomberg.

When February 15 came and millions of people gathered in cities around the world to oppose the looming war, New York hosted a debacle. First Avenue from the U.N. north was set aside for the rally, but since the NYPD decided to use metal pens for the demonstrators, the blocks quickly filled up with something between 100,000 and 400,000 people. Cops at barricades gave conflicting information on where people could go to enter the rally. There were scuffles as some demonstrators tried to push their way in. for blocks around the rally scene, thousands of people who could not enter the pens lined sidewalks. Seventy people filed complaints with the Civilian Complaint Review Board, 13 of which accused police officers on horses of using excessive force. The CCRB only substantiated complaints against two officers, but nearly half the cases were closed because the board couldn't identify the officer involved—in part because the NYPD withheld some of the videotapes it had shot of the event. Later, Kelly began putting identification numbers on horses so civilians could pinpoint which mounted officers had crossed the line. The commissioner, however, declined to punish one of the two officers whom the CCRB had cited for misconduct.

There were other demonstrations against the war in the spring of 2003. It later emerged that the NYPD Intelligence Division had developed a questionnaire for people arrested at these rallies—one that strayed into asking people about their political beliefs. This Demonstration Debriefing form asked protesters for the name of their organization and "organization position," as well as their "prior demonstration history." When Judge Haight learned about the use of the form, he seized back some of the leeway under the Handschu guidelines that he'd given the NYPD just a few months earlier.

Later in 2003, some of the protest groups that the city had foiled on the eve of the Iraq war began filing for permits to hold events during the Republican National Convention, to be held the following summer. United for Peace and Justice (UFPJ ), for one, applied for permits for both a march and a rally to take place the day before the convention was to be gaveled to order. After some negotiation, the group got its wish to march past the convention site at Madison Square Garden. But when it came to UFPJ 's plan for a rally on Central Park's Great Lawn for 250,000 people, the city said no. Two other groups working together, the National Council of Arab Americans and Act Now to Stop War and End Racism (ANSWER), were also turned down for a smaller demonstration of 75,000 on the lawn during convention week.

The reason? The Great Lawn had hosted massive gatherings (like the 1982 anti-nuclear march, which drew 700,000) in the past. But, the city said, since the $18 million restoration of the Great Lawn in the late 1990s, the parks department's policy was to prohibit large events there except for a limited number of traditional performances by the New York Philharmonic and the Metropolitan Opera. "Your event would cause significant damage to the lawn," the parks department wrote ANSWER. "Such damage would probably require the closing of the entire lawn for a significant period of time."

The activists were stunned. "We were just incredulous. We left those meetings scratching our heads," says UFPJ 's national coordinator, Leslie Cagan. "Did they really say it was about the grass? Did they really spend millions on fixing the grass and not think about large events?"

The city offered alternatives to ANSWER: Flushing Meadows-Corona Park in Queens, Van Cortlandt Park in the Bronx, the East Meadow in Central Park. These seemed a little too far from the action, or they were too small, so ANSWER refused. UFPJ asked for the North Meadow in the park, but the city said that wasn't a "suitable alternative." The NYPD offered UFPJ the West Side Highway instead; the group accepted then reneged when it learned that staging the event there would cost hundreds of thousands of dollars more, and UFPJ was unsure whether the city would provide water and bathrooms. So just days before the convention, the protest groups sued separately, claiming the parks department had denied their permits because of their political messages—not what they'd do to the grass. Even the New York Post thought the city had tilted the balance between first Amendment rights and the health of the grass a little too far in the turf's favor. "Sure—it is a great lawn. But it happens to belong to the people of New York City," the newspaper wrote. "And if the lawn is harshly used, the solution seems clear enough: Plant a new lawn. Grass seed is cheap."

But City Hall told the protest groups to "stop the theatrics." The problem, the city said, was that a political demonstration couldn't be ticketed, so there was no way to control the numbers. What's more, a rally couldn't be canceled in the event of rain, leading to severe damage to the lawn—like the $140,000 repair job that the Dave Matthews Band left behind in 2003. Federal and state judges accepted the city's arguments and scolded the protest groups for waiting too long to sue.

Later on, it emerged that the city had given inaccurate information to the judges. Some Great Lawn shows had gone forward despite wet conditions. And the city's claim that most Great Lawn events were now ticketed was "contradicted by the evidence," the judge wrote. He added: "There is evidence tending to show that rallies are categorically disfavored by [the city]…. There is evidence that permits were granted to preferred speakers based in part on the speaker's financial contribution." He cited a pre-RNC e-mail from Parks Commissioner Adrian Benepe that read, "We are gratified that [Bloomberg] supported the idea of not having rallies on the lawn in Central Park."

As it turned out, a few dozen protesters did make their way from the August 29 UFPJ march to the Great Lawn. Police stood aside and watched as the demonstrators attempted to sit in the shape of a peace sign. Not every encounter between law enforcement and RNC protesters went so smoothly.

Videotapes of the march on the second day of the convention (Tuesday, August 31) by the War Resisters League—one of the nation's oldest pacifist groups—from ground zero begin with a tall, white-shirted police commander, Deputy Chief Thomas Galati, speaking into a bullhorn. "If you do not follow the laws and regulations of New York State you will be subject to arrest. Please follow all traffic rules and march safely. I'll see you at Penn Station," he said. "Try to make your way over to the sidewalk so traffic can get through. Thank you."

The crowd began moving, being waved across Church Street by police. Some, but not all, of the marchers were planning to stage a die-in in Midtown, in which they would submit to arrest in acts of civil disobedience. It was not a permitted march—the WRL's philosophy is that the police do not have a veto on Americans' right to assemble peacefully—but as often happens, the organizers had struck a deal with the police to let the march go forward. The crowd bunched up as it moved along the sidewalk on Fulton Street; up ahead, the procession thinned out—it barely looked like a march, according to some. A few minutes later, another police commander, Deputy Chief Terence Monahan, approached the throng as it moved slowly along that first congested block of Fulton. He shouted that people weren't staying two abreast as organizers had agreed they would. "You are blocking the sidewalk. If you don't disperse, you'll be arrested," Monahan bellowed. Fifty seconds later, Monahan barked at the officers under his command. "Line it up! Line it up! Everyone from here on down is arrested." Since he was operating without a bullhorn, some protesters didn't hear Monahan. Even the cops looked confused. Some officers on Church Street kept waving protesters across the street, further bulging the crowd that had been blockaded by other officers standing at the front near Monahan. Protesters asked why they were being arrested. "The entire sidewalk was blocked," an officer said. "Warnings were given."

A surreal scene then unfolded. Monahan pressed a man who tried to leave back into the crowd. Press photographers were barred briefly from leaving the arrest zone. Bike cops stood with their cycles in front of them, forming a barrier to trap the 200-or-so protesters. Legal observers shouted instructions from across the street. A bare-breasted woman incongruously talked logistics over her cell phone: "I could be late for work right now." Several police officers with camcorders began slowly tracking around the block, filming those caught. In the confusion, pedestrians and other marchers wandered into the arrest zone. Galati had to tell the cops at the perimeter, "I don't want anyone caught in the middle of this who wasn't here in the first place." Then the bike cops gave way to officers rolling orange construction netting around the block to trap the people inside. Everyone within the net was arrested, 227 people.

A similar scene played out on at least two other occasions that day. One group of protesters was nabbed in orange netting at the New York Public Library. And along East 16th Street near Union Square, police netted off both ends of the street and arrested everyone who was there, including passersby and protesters who, even though that march was also unpermitted, may have been legally walking on the sidewalk.

Those nabbed in the nets were flexcuffed and put on buses; some waited on buses for hours, and on at least one bus a woman started vomiting. Eventually the buses delivered the detainees to Pier 57, a former bus depot, where they were put into pens. Some pens were too crowded to allow everyone to lie or sit down at once, so they took turns. Pier 57's environmental soundness as a holding cell for hundreds of people later came into question. So did the decision to hold them at all, as opposed to issuing summonses or desk appearance tickets, as was the usual practice during previous protests. Under a special RNC policy, the NYPD said everyone had to be detained, fingerprinted and arraigned. Some weren't arraigned for 40 hours or more. By the time the convention was finished, a state judge held the city in contempt for defying his order to release protesters it still had locked up.

Of the 1,806 people arrested at protests during the Republican National Convention, 22 pleaded guilty to misdemeanors like obstructing governmental operations. Twenty-one were convicted at trial of violations and 135 pleaded guilty to violations like disorderly conduct. Thirtyfive went to trial and were acquitted; 34 people were supposed to go to trial but never showed up. Judges dismissed 463 cases at the outset, and prosecutors declined to press charges against four people. The rest—1,092 of them—received "adjournments in contemplation of dismissal" meaning the case effectively vanished as long as they didn't get arrested again in the next six months.

A few of these arrests were a result of civil disobedience—people submitting to arrest as a form of protest. But many of the protesters who were hauled in did not intend to get arrested, at least not while merely walking up a street. Dozens of those arrested sued the city, arguing that the NYPD nabbed people—including people who weren't protesting—improperly and held them in dismal conditions on Pier 57 for too long. The length of detentions prevented some of the protesters from returning to the streets during the convention.

The city has defended its approach to the RNC by citing the threat of terrorism or violent demonstrators. But the NYPD has been reluctant to produce evidence of why it expected violent protesters—especially why it expected them to be lurking in the ranks of pacifist groups like the War Resisters League. In May 2007, on the order of the judge overseeing most of the post-RNC lawsuits, the NYPD released summaries of information collected by its pre-RNC intelligence operation. These documents show that the police developed detailed intelligence on not only the tactics of violent groups—who favored actions like throwing nuts and bolts at police officers—but also the beliefs and operations of mainstream, apparently peaceful organizations. It is clear from those documents that the police were doing more than reading websites; undercover sources whose names are blacked out provide inside information about, for instance, how many people had signed up for a train that UFPJ was sponsoring to the RNC. for months, the arrestees' lawyers and the city have been fighting about whether the NYPD must now release its raw intelligence reports on protesters. for much of last year, the NYPD pressed to have its intelligence chief, David Cohen, submit testimony that only the judge could see to explain why the NYPD should not have to produce those documents. The judge has rejected that idea. The NYPD also refused to allow the NYCLU to hand over documents to the FBI for the bureau's investigation of possible civil rights violations at the RNC. Meanwhile, the city has argued that environmental reports on Pier 57 should be withheld because they might contain diagrams that terrorists could use to attack the pier, and it has resisted releasing internal reports on the RNC because they "contain unguarded assessments and criticism by senior NYPD personnel that will cause embarrassment and mislead the public if publicized." for its part, the city has sought the War Resisters League's meeting minutes and mailing lists.

Some key NYPD personnel have yet to complete their depositions in those cases. One lawyer associated with the lawsuits says he does not expect a resolution until at least 2010. The city has so far paid out $1.5 million to settle RNC claims.

Those lawsuits weren't the only outgrowth of the way the NYPD policed RNC protests. So was the later series of battles between police and Critical Mass—pro-biking gatherings that have occurred in some 300 cities around the world and take place once a month around Union Square. After occurring without incident for years, an unusually large Critical Mass ride right before the RNC ended with 300 arrests. Over the next two years, hundreds more people were arrested or given summonses at the rides, which attracted a heavy police response: cops on scooters, officers wielding video cameras and undercovers among the bikers. The city even tried to get a court to stop the rides. When that effort failed, Kelly moved to change the legal framework under which he could arrest people assembling in the street by imposing new rules on parades in the city. His first proposal—to require permits for some processions of as few as two people, but generally for any procession of 20 or more bikes or 35 or more pedestrians—was quickly withdrawn. His second try, pegged to 30 cyclists or pedestrians, triggered a lot of opposition too. finally, Kelly decided last year on a straight 50-person rule. Anything bigger than that required a permit, or else participants could be arrested for "parading without a permit," which carries a jail sentence of "not more than 10 days." Kelly did not need or seek City Council approval to alter the rules. But Speaker Christine Quinn supported the change.

A coalition called Assemble for Rights NYC began negotiating with sympathetic City Councilmembers—Gail Brewer, Alan Gerson and Rosie Mendez—to change the rule. The three recently introduced a bill that would allow groups of up to 100 to gather without a permit, decriminalize parading without a permit and require the NYPD to provide a series of warnings before dispersing a crowd. The problem with Kelly's rule, Mendez says, is that "it was so sweeping that everyone got caught up in this regulation. It was so broad that it caught everyone." She says the police don't appear to be enforcing Kelly's new parade rules at this time. But they can start to enforce it anytime they like. State and federal courts are weighing whether the parade rules are unconstitutional. At Critical Mass rides nowadays, "the police are a lot less visible. Every year they become less visible. They seem to be assembling further away," says Bill DiPaolo, founder of Times Up!, an organization that supports the Critical Mass rides. "They're still there. They're just a lot less obvious." But DiPaolo blames the reduced popularity of the rides—they draw about 100 bikers now compared to nearly 1,000 at their peak—on the NYPD's enforcement at early rallies.

It's fair to ask why protest groups wouldn't simply get a parade permit. The answer differs depending on the organization involved. The whole point of Critical Mass is that it has no leadership or organization to seek a permit (which requires stating the "character of organization [social, political]" and answering the important question "Will rifles or shotguns be carried?"). Other groups are opposed to the idea that any part of government, particularly armed police, can limit or delay what the first Amendment allows. Getting a permit is cumbersome if the protest is a spontaneous reaction to some event.

Then there's a practical side. Police can veto a march route much more easily beforehand than when an organization has hundreds or thousands of people on the streets, ready to go. Several groups say they've met with resistance from the NYPD in getting permits.

Protesters and their supporters are split on the impact of the NYPD's approach to protest. UFPJ 's Cagan says the fight over the Great Lawn brought more publicity to the RNC protest than it might have otherwise received, but also prevented anti-war protesters from hearing the speeches that provide a coherent message to a large gathering. Some see an impact beyond the RNC. "The mass arrests, the delays in processing those arrested, these all dissuade people from expressing themselves," says Michael Ratner, president of the Center for Constitutional Rights. "After they throw a net over people, if you're a noncitizen, you're not going to come. If you're black or Hispanic, do you still come?" he asks. "How many people with children can afford to spend three days at Gitmo on the Hudson? It tremendously limited protest and civil disobedience."

Since the RNC, protest leaders say police have been more accommodating to demonstrations. NYPD commanders played it cool in December 2006 when they de-escalated a potential confrontation and allowed a crowd protesting the police killing of Sean Bell to hold a quick march near City Hall without a permit. At an antiwar protest in March 2007, the police commander on site was so chummy, he led the marchers in their chants. Chief: "What do we want?" Marchers: "Peace!" Chief: "And when do we want it?" Marchers: "Now!"

The city in January settled the Great Lawn suit, allowing a panel of grass experts to review the policy on events there. In a separate settlement, the city has promised to change policy on the use of pens and horses at protests. But the NYCLU's Christopher Dunn says he doesn't see a sea change in the city's approach to demonstrations. "We see the city fighting tooth and nail on the RNC cases," he says.

Bloomberg has defended his record on free expression and the NYPD's tactics at the RNC. He's even expressed a respect for demonstrators. "I think it's wonderful that they protest," he said of a recent anti-war demonstration. "I don't necessarily agree with them, but it would be a shame to have this freedom to express yourself and to try to influence government and then to be too lazy to use it." Last year, in a boost to free expression, Bloomberg pulled back from rule changes that might have required permits and insurance coverage for virtually all photography and film on the city's streets.

But overall, civil libertarians don't believe Bloomberg's performance has matched his rhetoric. "Bloomberg is not like Giuliani—a nasty person around first Amendment rights," Ratner says. "But you look at demonstration issues from the RNC to the WEF to the Iraq demonstration cases. These are terrible. I think we have crippled the first Amendment in this city. I am surprised by that." And the worries go beyond policing: Some activists are concerned that the parks department's plan to revamp the north end of Union Square will eliminate a traditional meeting place for the city's protesters.

If the city has cast a suspicious eye at protest since September 11, so has the federal government. The Pentagon's TALON database tracked political events like a November 17, 2004 demonstration in New York City that was described as a "possible threat to Air force recruiting station." Another, for February 3, 2005, was tagged "possible violent demonstration at NYU." Separately, the ACLU has obtained thousands of pages of FBI files on Greenpeace and the ACLU itself.

Inside the 2004 convention itself, federal agents took the lead in protecting the Madison Square Garden crowd and, it seemed, the GOP message. Secret Service men spot-checked people in the crowd, looking for anti-Bush signs intended to be unfurled during prime-time TV coverage. In one incident during the convention, two federal agents accompanied by two men wearing Bush/Cheney T-Shirts confronted a young man standing alone on a street corner outside the convention security zone. He held a poster of the hooded Abu Ghraib figure that read "Got torture?" The agents asked for his identification. He refused to provide it. When a reporter took notice of the scene, an MTA cop ordered him to move along. The guy with the poster got moved too. His protest was over.