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In the cover of darkness, an FBI SWAT team descended on the modest, one-story home in northeast Houston hours before dawn Thursday.

One group gathered in the front and a second assembled out back. In a side bedroom was the man they were trying to rescue, 47-year-old Ulises Valladares, who police say had been kidnapped the day before at gunpoint and was being held for ransom.

By the end of the operation, Valladares would end up dead at the hands of an agent's rifle — capping a chaotic turn of events that Houston Police Chief Art Acevedo called "tragic" on Tuesday.

"This is a tragedy you can't take back," he said at a news conference. "It's heartbreaking for everyone involved."

Acevedo said the department's use of force investigation is continuing before evidence can be presented to the district attorney's office for possible charges. He detailed how such a "dynamic situation" went wrong.

At about 3:30 a.m. CT (4:30 a.m. ET), as agents worked to get into the front of the home, another agent using a bar to breach a back window accidentally dropped the tool inside. He instead used an M4 rifle to get through the window, but felt something tugging at the gun from within the home. No one knew it was Valladares, who remained bound with duct-tape.

Fearing that he could lose control of the weapon, the agent fired two shots: One struck Valladares and the other entered the eaves of the roof.

"He made a split-second decision," Acevedo said.

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Related: FBI agent fatally shot kidnapping victim during Houston raid

Once the agents got inside, they found Valladares wounded. He later died at the hospital.

The police chief said the home was dark at the time, and that agents didn't use a light because they didn't want to inadvertently blind agents who were barging through the front.

"You can train all you want, but lighting conditions are lighting conditions," Acevedo said. "They made a tactical decision."

Avecedo said the FBI asked not to release the name of the agent who fired the gun. He was placed on paid administrative leave pending the outcome of the investigation.

Other people, including children, were inside the home during the raid, but Acevedo declined to speculate as to why the agent blindly fired.

The FBI did not immediately respond to the details released by Houston police or comment on the actions made by its agent. In a previous statement, the agency said it "takes very seriously any shooting incidents involving our agents and as such have an effective, time-tested process for addressing them."

Acevedo said that while Valladares was killed by the FBI, those who orchestrated his kidnapping are still culpable.

"If he had not been kidnapped, we wouldn't be having this conversation," he added.

Valladares had been held in the home of Sophia Perez Heath, 35, one of three people arrested in the case, according to a court affidavit. Police said Heath's boyfriend, Nicholas Chase Cunningham, 42, and a second man, Jimmy Tony Sanchez, 38, kidnapped Valladares last Wednesday morning from his home in the Houston suburb of Conroe.

During the kidnapping, Valladares' 12-year-old son was also home, getting ready for school. The father and son were bound with duct-tape, and the son had overheard the men saying that Valladares' brother owed them $8,000, according to court documents.

From left, Jimmy Tony Sanchez, Nicholas Chase Cunningham and Sophia Perez Heath. Conroe Police Department

The men ransacked the home for valuables, police said, grabbing a PlayStation, an Xbox, a sword and hat. Leaving the boy behind, the pair eventually took Valladares to Heath's home, where she was told to watch and feed him.

Police were called after the son broke free from his restraints, and the FBI was alerted to help find Valladares.

Valladares' brother received a ransom call that was linked to Cunningham and Sanchez, police said. The investigation eventually brought the FBI to the tiny home on Elbert Street where Heath lived.

During a court hearing Friday, Cunningham and Sanchez were denied bond. A judge set Heath's bond to $1 million, and must wear an ankle bracelet if she makes bail.

Acevedo said that a civil case could also be brought forward in Valladares' death.

"I think if the FBI were allowed to talk about it on the local level, they'd tell you their hearts go out to the family," he added.