"It wasn't a question of what career you were going to choose, it was a question of whether the country would survive a war," said student activist Juan Gonzalez. The protests began on April 23rd, 1968 as an outdoor demonstration in Columbia's main quad. Students of two groups, the Student Afro-American Society (SAS) and the Students for a Democratic Society (SDS) felt their separate causes intertwined on that day. Students moved the protest inside and stormed Hamilton Hall. The acting dean, Henry S. Coleman, was held hostage in his office. Despite their initial unity, it quickly became clear that the two groups had vastly different aims.

The Student Afro-American Society protested the proposed construction of a gym in neighboring Morningside Park. They referred to this as "Columbia's Gym Crow," criticizing the University's seizure of public land and the design of the facility, which they argued was segregated. Only 12% of the gym would be for Harlem residents, and they would have to enter through a separate door at the bottom of the park (protesters called this the g-y-m crow door). The black student's outcry stemmed from Columbia's failure to address the assassination of Martin Luther King Jr. earlier that month. Furthermore, they claimed that Columbia's treatment of black students was still inherently racist, despite claims of equality by administrators. The group's activities were peaceful, drawing from sit-ins and silent marches from the civil rights movement

The other group, the SDS (Students for a Democratic Society), protested Columbia's involvement in the Vietnam War. Bob Feldman, a member of the SDS, had uncovered documents detailing the school's involvement in a weapons think-tank, the Institute for Defense Analyses. In response, the SDS launched an anti-war campaign, of which this protest was a part. They demanded Columbia's resignation from all affiliation with war-related missions and weren't afraid to use force to obtain these goals. It was SDS that had held the Dean hostage (though only for one day.)

Though the SDS and the SAS saw the timing of their causes in alignment, it quickly became clear that they would not be able to proceed towards their goals without conflict. Black students of the SAS asked all white protestors to leave Hamilton Hall. This move was largely strategic: the University and the police would be weary of storming a building peacefully occupied by only black students. Furthermore, the SAS had previously aligned themselves with tenants-rights and other community groups and were aware that these allegiances gave them the protection of the entire neighborhood of West Harlem. The SAS chose to focus their demands on the gym. They set up the "Malcolm X Liberation College," in Hamilton Hall and opened their doors to black visitors and speakers.

The SDS and other White students moved into Low Memorial Library, where they occupied the president's office. Three other buildings were occupied by the SDS, though the library was the most significant base for the movement. Outside the library, a "majority coalition" of around 300 undergraduate students formed a human blockade around the building. They disagreed with the actions of the students, though not the cause itself.

The protest ended on April 30th, at 2:00 AM. The University called for 1,000 police officers to storm the campus. The administration was fearful of violence erupting between students, or worse, between the community and the University. There were over 700 arrests and 100 injuries. The black protesters from the SAS in Hamilton Hall were cleared out peacefully, while SDS members fought and struggled with the police force. In response to the event, Columbia disaffiliated with the IDA and worked on an alternative plan for a gymnasium elsewhere on campus. Frank Guidry, a history professor who leads tours of sites related to the protest, suggested the University visibly commemorate the movement. "They should put a plaque...it should say, ‘This event happened. It was difficult and violent. But it made our community a better place.'"