After a lockdown that lasted more than an hour, the university issued an "all clear" after an earlier emergency notification that an "armed and dangerous" person was on or near campus.
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A short time later, ABC11 was the only news outlet at the scene where officers made an arrest about 2:45 p.m. at a Greenfield Place apartment building in the 300 block of Formosa Lane.
WATCH: Exclusive video as suspect taken into custody
Person taken into custody after UNC incident
Chapel Hill Police identified the man as Mickel Deonte Harris, 27, of Durham.
They said Harris was arrested on outstanding warrants related to an assault on Sept. 5 in Chapel Hill and was also sought in connection with Wednesday's incident on UNC-Chapel Hill's campus.
Harris has a lengthy criminal history, ABC11 has learned. The Chapel Hill Police Department is leading the investigation.
Harris was booked at the Chapel Hill Police Department and then was placed in a squad car presumably to be taken to the Orange County Jail.
Charges against Harris are pending.
In an alert issued at 12:54 p.m., the university advised students and staff to stay inside and close windows and doors immediately until further notice.
UNC Campus given all clear after alert
At 2:11 p.m., UNC said it was safe to resume normal activities and that the lockdown had been lifted.
The investigation appeared to center on Alpine Bagel in the Student Union. Law enforcement said it believes that this is an isolated incident.
UNC Campus Police Chief Brian James said authorities believe there was some connection between Harris and the bagel shop. He said the motive for the incident wasn't yet known.
Witnesses told ABC11 that a man got into an altercation with the cashier. Witnesses said it did not appear that the cashier was a student.
Witnesses said that during the apparent argument, the man pulled out a gun and pointed it at the cashier's head. No one heard any shots and some people began dialing 911.
"I was in Alpine when I was having my lunch and then I left and not five, 10 minutes later, some guy comes through on a bike and he's telling us all to run inside and so we did," said Kareem Adel, a UNC junior.
WATCH: UNC Police, chancellor give update on campus gun scare and arrest
UNC Police, chancellor give update on campus gun scare and arrest
James said witnesses told authorities that Harris confronted a worker, displayed a firearm and threatened an employee before leaving the scene in a vehicle.
Alpine Bagel closed early for the day.
No one was injured in the incident.
James said police are reviewing camera footage.
"Everyone responded as they were supposed to. Our UNC police officers organized themselves, went into buildings to clear areas and our partners got here quickly to establish a perimeter around campus to help us clear buildings as needed," he said. "We stand here again hoping this never happens again."
The University canceled all classes for Wednesday and all offices and facilities were closed. UNC was expected to resume normal operations on Thursday.
"The news of another armed person and a second lockdown on our campus is concerning and can be traumatic," UNC Chancellor Kevin Guskiewicz said. "I want to be clear, that guns are prohibited on this campus and every campus across the state of North Carolina."
The University advises the campus community to go to alertcarolina.unc.edu, for updates.
WATCH: Students describe what they saw and heard
UNC students talk about campus lockdown
CHAPEL HILL-CARRBORO SCHOOLS
All CHCCS schools operated in a "Secure Mode" during the UNC lockdown, which meant that the doors were locked and people were not allowed in or out but that classroom instruction could continue normally inside.
WATCH: Chapel Hill-Carrboro Schools operate in 'secure mode' after UNC lockdown
Chapel Hill-Carrboro Schools operate in 'secure mode' after UNC lockdown
After the "all clear" was issued, CHCCS said schools were exiting "Secure Mode" and dismissal at elementary schools would begin at the usual time of 2:35, though it may be slightly behind schedule.
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Middle schools and high schools were dismissed at their usual times. Afterschool activities and Community Schools After-School Care took place normally.
SECOND UNC LOCKDOWN IN 16 DAYS
This is the second time within three weeks that campus police and the university have issued a Carolina Alert and locked down the campus.
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On Aug. 28, the alert was issued after a student allegedly shot and killed his professor.
University of North Carolina graduate student Tailei Qi has been charged and indicted with killing Associate Professor Zijie Yan in Caudill Labs.
The gun allegedly used by Qi has yet to be recovered, according to UNC police.
UNC students have expressed frustration and outrage and how the school handled communication, the alerts and the release of information.
On Wednesday, students lamented the state of affairs on UNC's campus.
"A lot of us were in the same classes today that we were in two weeks ago when the situation happened," said student Sydney Ross. "So, it's it's just it's really sad to see. But I will say that I'm grateful for the people that we were sheltered with today just because we were all supporting each other in the situation because it's a scary situation to live through."
Another student, Luke Diasio, said he was taking a test when he heard the sirens, He said he then heard about the text alert that an "armed and dangerous" person was on campus.
But Diasio said it's not enough to make him feel safe on campus.
"It's very difficult to organize a coordinated response but there's got to be something faster than this," Diasio said. "There needs to be a singular way in which they can rapidly communicate because this is not going to cut it."
James said that reported incidents have to be confirmed "from a law enforcement perspective" before a full lockdown is issued. He said false calls have been made on other college campuses across the country in the past.
"It is important that we go to the location and actually confirm before we issue a lockdown notification," James said.
Just minutes before the incident, an online survey was launched asking students for their feedback after the Aug. 28 deadly shooting, and how communication and campus safety can be better handled.
Diasio said he wants to see more lawmakers involved when it comes to finding solutions for safer campuses.
On Tuesday, UNC Chapel Hill students met with lawmakers about solutions to gun violence.