The child's mother, Jasmine Salas, is in jail after being accused of playing a role in his abuse.
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Salas is charged with injury to a child, a first-degree felony, and is held at the Harris County jail on a $150,000 bond.
The family of the 3-year-old, Nehemiah, told ABC13 on Tuesday that he is in a coma.
His family told Eyewitness News that Nehemiah is suffering from severe malnourishment, a burn on his head, bruising, and broken ribs.
"They're telling us we don't know if the chances of the smiling baby, we may never see that again. And I just can't imagine that," Nehemiah's great aunt, Emma Schiefer, said.
On Friday, Schiefer said their family got the news their smiling boy was flown to the hospital. She said they didn't know how bad his injuries were until they were allowed to see him at the hospital on Saturday.
"A 3-year-old should have never have had to have gone through this," Schiefer said. "I was in shock to see him having a neck brace...the tubes, the things on his head, all the sensors, everything, and to find out he's in a coma."
Court documents show Nehemiah's mother is accused of knowing her boyfriend was beating up her 3-year-old son and didn't intervene or seek help.
The court revealed that Nehemiah suffered a severe burn to the crown of his head, subdural hematoma, bruising on his entire body, swelling to the face, extreme malnourishment, liver lacerations, bruised lungs, rib fractures, pleural effusion, subconjunctival hemorrhage, and preorbital ecchymosis.
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The Houston Police Department would not release her booking photo to ABC13, citing the open investigation.
Court records reveal the man in question is not the child's father. Instead, he is a person law enforcement refers to as a co-actor and has not been charged.
"To do that to a child, she deserves to stay where she's at and never get out," Schiefer said.
Schiefer is the biological father's aunt. She said she doesn't know Salas' boyfriend, who is accused of being a co-actor in the abuse of the 3-year-old. Schiefer said Salas was supposed to care for and protect the child.
Schiefer says if the boyfriend did play a role, then she hopes he is held accountable.
Sources told ABC13 that a second boy, Nehemiah's older brother, is in Child Protective Services while case workers figure out what's best for the boys.
The family is unsure, at this point, if the 5-year-old was also hurt or if he had to witness what happened to his 3-year-old brother.
Their great-aunt said she hadn't been able to see the boys in several weeks and hadn't seen Nehemiah since November. Schiefer says seeing Nehemiah lying in the hospital so defenseless and hurt has been devastating.
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CPS would not reveal if there was prior history between Salas and her children.
There are still so many questions about how, why, and how long this has been happening.
The family wants justice, but their priority right now is Nehemiah's recovery. They're praying for a miracle.
"He did open his eyes yesterday when we were talking to him. It gives us hope. It gives me hope that he's still there. That he's still in there beneath all that trauma," Schiefer said.
Schiefer wants to see her energetic and lovable grand-nephew smile again.
If you'd like to help the family with the 3-year-old's hospital expenses, you can do so by visiting their GoFundMe.
For updates on this story, follow Daniela Hurtado on Facebook, Twitter and Instagram.