Hundreds of protesters took over a large swath of Grand Central Terminal during the peak of the evening rush hour, displaying their displeasure at the MTA's fares and increased police presence in subways.

The NYPD had prepared for possible disruptions across the city's transit system throughout Friday after the group announced a mass gathering to call for an end to targeted harassment by police.

Ahead of the evening commute, Metro North alerted riders that they may "experience increased crowding and street closures due to potential demonstrations," advising them to avoid the area or take earlier trains if possible.

While there were some heated moments at Grand Central in the evening, the majority of the protests appeared to be peaceful, albeit a disturbance for commuters looking to catch their trains home. Several participants were arrested both inside and outside the transit hub, as some were blocking traffic.

A large group of protesters filled Grand Central terminal as they protested the MTA's fares and the agency's decision to increase police patrols of subways. NBC New York’s Ray Villeda and Myles Miller report.

According to law enforcement sources, there were around 500 protesters who gathered, with 15 arrests made at the terminal. The graffiti found in the subway stations across the city is being investigated by the NYPD's transit vandals task force, sources said.

In addition to anti-MTA messages getting scrawled on station walls, there were also new mobile readers at turnstiles disabled and gorilla glue placed in MetroCard readers.

Around 5:30 p.m., the protesters moved from Grand Central and took to the streets, making their way to the Bryant Park and Times Square subway stations. All entrances to to the station were reopened by 6 p.m.

After the midtown protests, the group took different subway lines and reorganized in Brooklyn, along Fulton Street in Bed-Stuy. Streets in the neighborhood were full of protesters, who continued demonstrations into the night.

One woman was hurt after a police believe a hammer was thrown through a restaurant window on Fulton Street in Brooklyn. The protester who threw the hammer has not been caught.

MTA Chief Safety officer Patrick Warren released a statement regarding the protest, saying it "follows the dangerous pattern of previous activities that have resulted in vandalization and defacement of MTA property – clearly violating laws."

The statement went on to criticize the actions as diverting "valuable time, money and resources away from investments in transit services that get New Yorkers to their jobs, schools, doctors and other places they need to go. The MTA has zero tolerance for any actions that threaten the safety of the public and our employees, and impede service for millions of customers."

Protesters led a large demonstration at Grand Central at the peak of the evening rush hour, then went on the move en route to Brooklyn. NBC New York’s Myles Miller and Marc Santia report.

Among demands of free transit and full accessibility in subways, Decolonize This Place encouraged New Yorkers to show up and move as a group to dismiss the MTA's $2.75 fare and advocate against cops in the transit system.

"The streets are ours. The trains our ours. The walls are ours. This moment is ours," the group said in a Twitter post accompanying its announcement video.

Protests were expected to take place over the course of the day -- and cops said they were prepared at all hours. Some subway access doors were chained open to allow people to go through without paying the fare. Profanity-laden graffiti already was scrawled on some subway stations before the sun fully came up, and more was found throughout the day.

In an internal memo obtained by NBC New York, NYPD Chief Terence Monahan on Thursday told command staff, "While we will always protect people's right to protest, illegal conduct that puts law-abiding community and cops in danger will not be tolerated in New York City."

"It is imperative that officers take appropriate action and make arrests when they observe a violation of the law," he continued.

Also in Monahan's memo, he said the group "will attempt to disrupt public transportation, cause disorder - and physically assault police officers."

The clashes between protesters and police got violent at times, with some demonstrators vandalizing buses and police vehicles with anti-police messages. The protest was in response to recent arrests of food vendors in the subways, and other incidents. NBC New York’s Myles Miller reports.

Friday's gathering is the third one organized by Decolonize This Place. In November, dozens were arrested after a huge crowd of about 200 protesters converged in Harlem, with some of the participants leaving buses and police vehicles vandalized with anti-police messages.

During the morning commute, some confrontations with officers turned violent but no injuries were reported.

The rallies have been in response to the NYPD's presence and arrests in the subway, specifically against low-income New Yorkers and people of color.

Despite the outrage that has been growing in Brooklyn over the video, NYC Mayor Bill de Blasio said he reviewed the video and believes the officers involved handled the situation appropriately. NBC New York’s Jamie Roth reports.

Earlier this month, New York Attorney General Letitia James announced that her office is investigating the NYPD's fare-enforcement practices after the department found black and Hispanic people account for the majority of fare-related summonses and arrests.

"We've all read the stories and seen the disturbing videos of men, women, and children being harassed, dragged away, and arrested by officers in our city's subway system, which is why we are launching an investigation into this deeply troublesome conduct," James said in a statement.

NYPD spokeswoman Devora Kaye said officers "patrol day and night to keep 6 million daily riders safe and enforce the law fairly and equally without consideration of race or ethnicity."

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