The stranger accused of taking the girl from her parents' apartment has now been charged.
Holman Hernandez, 50, is charged with aggravated kidnapping.
It was only thanks to a witness that investigators had any idea who they were looking for.
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ABC Houston affiliate KTRK was there as police surrounded a motel and arrested the suspect on Sunday.
ORIGINAL REPORT: Missing 3-year-old girl last seen in north Houston located safely, HPD says
Police said Hernandez -- the suspect at the center of an Amber Alert -- put up a little bit of a fight after he was found about 2 p.m. at a motel with the little girl, just minutes away from where she was abducted.
According to court documents, Hernandez lured the child into his vehicle, kidnapped her and took her to a motel, where authorities found them both in bed. Hernandez was allegedly only wearing boxers while the girl was in a shirt and a diaper.
Officers had to force entry into his motel room.
"Officers approached the room, knocked on the door. The suspect didn't answer, and because of the age of the kid, officers forced entry into the unit," Houston Police Chief Troy Finner said. "Once they got in, the kid was observed inside with the suspect."
Several officers who were off were called in to help canvas the area after the girl's parents reported her missing from their apartment, according to Finner.
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They told police they went to sleep around 11 p.m. on Saturday and woke up around 5:30 a.m. Sunday to find their door wide open and their daughter missing.
As officers canvassed the neighborhood, a neighbor told them they spotted the girl with the suspect. Their testimony helped police determine exactly who they were looking for.
Police said they saw the suspect's car parked at the motel. Management told them the suspect checked into a room around 7:30 a.m.
Officers don't believe there is any connection between Hernandez and the family.
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"I can't imagine what they are going through, with a few hours not knowing where their little baby girl is," Finner said. "It's just tough. But we're so glad, blessed. Thank God the baby is OK."
The little girl was immediately taken to a hospital by ambulance to get a medical exam.
The charge against Hernandez was posted on Monday morning.