The 16-year-old was being sought and was arrested Thursday morning by members of the U.S. Marshals Regional Task Force.
Detectives learned he was at his apartment on West 172nd Street in the Bronx, where he lives with his mother, and were waiting for him as he was leaving.
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He was charged as an adult with one count of murder, five counts of attempted murder and one count of criminal possession of a weapon, according to police.
The 16-year-old was previously arrested for an attempted robbery in the Bronx in April 2023. At the time, he was linked to a local gang.
Six people, mostly innocent bystanders, were shot around 4:30 p.m. on Monday while waiting on the northbound platform for the No. 4 train at the Mount Eden train station.
Investigators believe there were three gunmen who fired at least 19 rounds, both inside the train and on the platform.
They believe the 16-year-old and another man were shooting northbound while the third gunman, a member of a rival gang, was shooting southbound.
Police now believe they have two out of three suspects in custody.
The victims ranged in age from 14 to 71.
One of those victims, 35-year-old Obed Beltran-Sanchez, was killed.
"One bullet hit him in the chest. He died almost immediately," said Jorge Islas, Consul General of Mexico in New York. "And with that, that bullet, life on a dream, someone who was willing to do something important for his family."
Islas says Beltran-Sanchez left behind a wife and two young daughters. It is believed he was a migrant from Mexico who crossed the border from Canada in search of construction work as a day laborer.
"He can buy a little house for his family. And he was willing to work hard in American New York, and over time, retire and go back to Mexico to work on Puebla and eventually live in the house that he was willing to build," Islas said.
Speaking from her home in Mexico, Beltran-Sanchez's widow expressed having to struggle with this unfortunate reality.
"All I want is for him to come back to me. With his parents - his parents are also suffering. His brothers," she said.
The injuries to the other five -- a 14-year-old girl, 14-year-old boy, 28-year-old man, 29-year-old woman, and 71-year-old man -- are not believed to be life threatening.
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The victim with the most serious injuries is the 29-year-old woman who was shot in the face and neck.
Police believe the shootout was gang-related, stemming from a dispute over drill rapping and disrespect. Investigators are now scouring over their social media.
The two groups are believed to have come together in a chance encounter on the train. One group boarded at 125th Street in Manhattan and the other at 161st Street in the Bronx, near Yankee Stadium.
A 14-year-old boy who was struck in the thigh and ear by the gunfire is also believed to have opened fire on the train. His role in the shooting is also being determined.
As that investigation continues, the 14-year-old was charged Wednesday with shooting a 15-year-old boy on Jan. 15 at Davidson and West Tremont avenues in the Bronx. The 15-year-old boy survived the shooting.
Detectives believe the gunfire on the subway train Monday could be retaliation for that January shooting.
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"Gang violence such as this senseless shooting resulting in death and injury to innocent citizens of the City of New York waiting for their train to get home will not be tolerated," said Ralph Sozio, the U.S. Marshal for the Southern District of New York. "We will use all the resources at our disposal to find you and bring you to justice to make our streets safe again."
Anyone with information is asked to call Crime Stoppers at 800-577-TIPS.
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