The boys, ages 3 years old and 11 months old, were found with multiple stab wounds submerged underwater in a tub with clothes over their bodies, according to police.
Their mother, Dimone Flemming, was charged Monday with two counts each of murder, intention to murder and depraved indifference.
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Neighbors who live down the hall say they heard the couple arguing and screaming Friday night.
The father of the 11-month-old boy allegedly slept in a car outside of the apartment after the argument because Fleming told security to not let him back into the building, according to police.
Officers first responded to a 911 call to the third-floor apartment on Echo Place where they say they found Fleming inside naked, acting erratically while trying to burn things in the kitchen.
Frances Pimemtel crossed paths with the mother outside before the call, and says Fleming was repeatedly saying "what I did."
Officers were told the woman's two children were with their father, so they took Fleming to the hospital for evaluation.
The father heard what happened and rushed into the apartment where he allegedly found the children in the tub under a pile of clothes.
Neighbors heard the father screaming for help and called 911 again.
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"He was screaming hysterically," neighbor Shannon Holyfield said. "He was screaming, 'Help me!' And I came and opened my door and I see him coming down the hall with the two boys in his arms. They were dead, they were dead. There was blood everywhere."
Officers and another family member attempted to resuscitate the boys, who were rushed to Columbia Presbyterian Hospital where they were declared dead.
Detectives believe Flemming stabbed her children in the neck and torso, although an autopsy will determine if they died from those wounds or from drowning.
NYPD hold update on stabbing deaths:
Police hold update after 2 children stabbed to death in the Bronx
"It's something that they are going to have to live with and think about probably for the rest of their lives," NYPD Deputy Chief Louis De Ceglie said. "We have very experienced police officers. I think they are the best. They are able to handle and cope with any situation."
Flemming's father said he spoke with his daughter hours before the killings.
"I never saw any red flags, she didn't give me any indications that she was going to harm herself or her kids," Dwane Flemming said.
He and others feel more could have been done.
"If my daughter was struggling with mental health, how come these social workers at the facilities shew as in didn't recognize any of this," Flemming said.
A memorial was started outside the shelter in memory of the two young victims. Neighbors lit candles, left flowers and hung balloons.
Friends and family are rallying around the father. He said he is not ready to talk, but says he does want the truth out there.
Fleming remains in the hospital under a psychiatric evaluation.
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