Christopher Michael Rickerson, 22, is charged with intentional child abuse causing serious bodily injury.
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According to an arrest warrant, the injuries happened at a home off Trail of Merlin Road near Garner October 24.
Rickerson - who is the boyfriend of the girl's mother - allegedly told authorities he was watching the child when she bumped her head on a dresser.
Officials say doctors examining the child said her injuries did not match the mother's boyfriend's story. The 2-year-old had a life-threatening skull fracture, along with old injuries to her foot and ribs.
The girl's father spoke exclusively with ABC11 last week.
"I believe no parent should go through what I am going through right now," Raul Trejo said.
He drove to the Triangle from Arkansas after hearing the allegations involving his wife's boyfriend.
Exclusive: Father of hospitalized toddler speaks out
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He said for more than a week his youngest daughter had been in a medically induced coma in ICU at Duke University Hospital.
Trejo says doctors were slowly taking her off medications to see how she would respond.
And then Thursday, Trejo said, he received a glimmer of hope in her recovery.
"I heard her cough," Trejo said.
GoFundMe page for Abigail
Deputies have also confiscated several items from the home: drug paraphernalia, a broken hairbrush, and phones belonging to Rickerson and the child's mother.
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Authorities are investigating the possibility of collusion or a cover-up.
ABC11 asked Trejo whether he thinks his wife is connected in covering up the child's injuries.
"That's a real tough question," Trejo said. "I hope she doesn't. She is a loving mother when I was with her. I honestly don't think she has anything to do with it."
Trejo said he has no words for Rickerson.
This case is still under investigation.
The family has set up a GoFundMe page to help with the child's medical expenses.