(CNN) Less than a week ago, an FBI agent fatally shot a kidnapping victim he was trying to rescue. On Tuesday, authorities provided an explanation for how things went so wrong.

The agent was part of an FBI SWAT team that raided a house early Thursday morning in an attempt to locate Ulises Valladares, who'd been kidnapped by armed men the day before, Houston Police Chief Art Acevedo said Tuesday at a news conference.

Two agents in the back of the house were breaching a window when one agent dropped the tool he was using, Acevedo said, so the agent started trying to breach the window with his assault rifle.

"Tragically and sadly, Mr. Valladares was right by that window and he was bound and obviously with his hands in front of him ... and he actually grabbed the rifle, our investigation is showing so far, and started to pull at the rifle," Acevedo said. "When (the agent) felt he was starting to lose control, he discharged his rifle, striking Mr. Valladares."

When the agents got inside the house, they discovered the man who'd been shot was the one they'd come to save.

"It is a tragedy all the way around," Acevedo said.

The agent, who has not been identified, was placed on leave while the FBI and Houston police investigate the shooting.

Three people have been charged in connection with Valladares' kidnapping and two of them may be charged with murder in Valladares' death, authorities have said.

Nicholas Chase Cunningham, Jimmy Tony Sanchez and Sophia Perez Heath were charged with aggravated kidnapping. The men also were charged with aggravated robbery.

Kidnapped at home

Valladares, 47, was abducted Wednesday morning when two men burst into his house in Conroe, about 40 miles away from Houston, as his 12-year-old son got ready for school, the Montgomery County District Attorney's office said in an affidavit to support arrest warrants for the suspects.

The men claimed Valladares' brother owed them $8,000, and bound Valladares and his son with duct tape, the DA's office said. After the men took Valladares away, the son escaped his bonds and called police, the DA's office said.

The brother, Ernesto Valladares, received a call from a man saying he was with a drug smuggling group, El Cartel del Golfo, or Gulf Cartel, and demanded $20,000 for return of Ulises Valladares, according to the DA's office. The claim of the cartel connection turned out to be untrue, authorities have said.

FBI agents tracked the phone used in the call to a Best Western motel where a cousin of Valladares was living with her husband, who matched the description of a kidnapper, the DA's office said.

At the motel, officers arrested the husband, Nicholas Chase Cunningham, 42, and Jimmy Tony Sanchez, 38, the DA's office said. They were both charged with aggravated kidnapping and aggravated robbery.

One of the men said Valladares could be found at a house in northeast Houston. Authorities raided the residence around 5 a.m. ET Thursday.

Agent fired two shots

At the news conference, Acevedo said FBI agents entered the house through the front door while two agents tried to breach a window that led to a room where Valladares was thought to be.

There was no lighting in back of the house or inside the room, and the agents didn't use lights because they didn't want to blind agents entering through the front of the house, he said. They yelled "FBI!" and deployed flash grenades designed to disorient people during raids, Acevedo said.

Acevedo said nobody knows why Valladares grabbed the gun.

"If I had to speculate, he was trying to get out of that room," he said.

The agent fired two rounds, one that hit Valladares and one that hit the ceiling, the chief said. Valladares was taken to a hospital, where he was declared dead.

The Harris County Medical Examiner confirmed to CNN that the manner of Valladares' death was homicide, and the primary cause of death was a gunshot wound of the left upper extremity with re-entry of the torso.

A third suspect, Sophia Perez Heath, 35, was arrested at the house and charged with aggravated kidnapping. At least one child was inside the residence, the chief said, but no other injuries were reported. Police have not said if anybody fired weapons at the FBI SWAT team.

Cunningham, Sanchez and Heath had a bond hearing Friday. Cunningham and Sanchez are scheduled to be back in court Wednesday, and Heath is scheduled for Thursday.

The investigations

Acevedo said the police department investigation will focus on this question: "Was the decision to fire two rounds objectively reasonable?"

The police will present evidence to the Harris County district attorney, who will decide whether to pursue criminal charges, Acevedo said. The FBI is cooperating and the agent has given a statement to police, he said.

The FBI's Shooting Incident Review Team (SIRT) is also investigating and will provide its evidence to the Department of Justice, the local police department and District Attorney's Office, the FBI said in a statement.

"The FBI takes very seriously any shooting incidents involving our agents and as such have an effective, time-tested process for addressing them. In the interest of protecting the investigation's integrity, we cannot comment regarding investigative details," the statement said.

The Conroe police and the Montgomery County District Attorney's office will investigate and prosecute the kidnapping and robbery at Valladares' home, Montgomery County District Attorney Brett Ligon said.

Ligon said Cunningham and Sanchez may be charged with murder in Valladares' death.

"The kidnappers put this into play and so they're ultimately responsible for the outcome," Ligon said.

CNN has not able to contact lawyers for Cunningham, Sanchez or Heath.

Seeking custody

Valladares' son is now under the supervision of child protective services but his uncle is seeking custody, said Douglas Ray York, a lawyer for Ernesto Valladares, according to CNN affiliate KPRC

The boy's mother died two years ago of cancer, York said.

"He is having to repeat the grieving process," York said of the boy. "His mother passed away. Now his father passed away and the FBI came in and basically made him an orphan."

Ernesto Valladares hasn't talked to his nephew since before the shooting, York said, according to KPRC.

"My client doesn't even know where the child is. He knows the child is in foster care, but there has been no communication, no contact, nothing, no visits, nothing," York said.