Police said they were pronounced dead around 10:45 a.m. inside a residence on Palisade Street near Lily Pond Avenue in the South Beach neighborhood.
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Police responded to the scene after receiving a call about an assault in progress and discovered a smoke-filled home. The FDNY responded and extinguished the small fire.
Officers found the bodies of a 36-year-old women and her two children, a two-year-old boy and a 3-year-old girl.
Sources familiar with the investigation said they were discovered face down on a bed and the children may have been drowned.
Investigators said a man, believed to be the children's father, was found wandering near the Brooklyn-Queens Expressway in Bay Ridge around 7:40 a.m. that morning. He was transported to an area hospital for an evaluation.
No charges have been filed.
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The identities of the suspect and victims have not been released.
Sources said both the victim and the suspect were active duty Air Force personnel assigned to the Fort Hamilton, Brooklyn base.
Sources said a co-worker in the Air Force discovered the bodies.
The Medical Examiner will determine the cause of death, but a homicide investigation is ongoing.