The incident happened on Sept. 18, just over two weeks after the same student was arrested for allegedly assaulting his classmate.
ORIGINAL REPORT: Parents question use of metal detectors after Texas City HS student found with gun on campus
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According to the student's father, the fight that happened on Sept. 1 catapulted the incident.
The 16-year-old was arrested for that incident as well, according to the Galveston County Sheriff's Office.
The Texas City Independent School District said federal law forced their hand. They had to let him back on campus because he was considered different than the general student population.
"He is in special education, and you know this is the whole issue. We told them when we enrolled him in school about all his problems and where he came from," the student's father said.
ABC13 concealed the identity of the father to protect his son, who is a minor.
The boy's stepmom told ABC13 that after the fight, her stepson was bullied by the boy he assaulted.
RELATED: Texas City HS student arrested for assault 3 weeks before bringing gun to campus, deputies say
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"This kid was threatening to shoot him and was threatening to have him jumped," the student's stepmom said.
ABC13 checked with the Texas City Independent School District, and it told us an investigation was conducted in this case, and they reported the findings to the parents of both students.
Seventeen days after the fight, the boy brought a loaded gun to school and was arrested again, according to the sheriff's office.
The father said a friend who was staying with them kept a gun inside his car, and his son took it.
"This is a situation that could have gone way worse. We are apologetic and wish we caught this and helped in any way we could, but you know he slipped through the cracks," the father said.
The father says before coming to Texas City High School, his son had been in child protective services for most of his life.
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"He's a good kid, you know. He has a very troubled past, and he's had a very hard life more than anyone," the boy's father tearfully said.
"I don't want to see him like this. I don't want to be visiting him in jail," he added.
The father says his son had post-traumatic stress disorder, and he said that from the start, they informed the school he could get violent.
He said his son is facing three charges for assaulting the student, the deputy, and bringing the gun to school.
Currently, he's being held in a juvenile detention center.