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Rhys Jones flew in from New York on Saturday to try to protect his mother from his father, who had been arrested last week for beating her and keeping a loaded gun in their apartment.

His instincts were right.

Bonnie Jones filed for an order of protection against her estranged husband after that incident, and her son had arranged for her to stay with friends. But when mother and son returned to her Rogers Park apartment Sunday afternoon to pick up belongings, Howard Jones leapt from a darkened bedroom doorway wielding two knives, police said.

The former physician stabbed his wife and son repeatedly and in the struggle, the three stumbled out the back door and down into the courtyard before Rhys Jones was able to get one of the knives away, police said.

Rhys Jones, 32, received several knife wounds, but it was too late for Bonnie Jones, 65, a school administrator at Clemente Community Academy High School in Humboldt Park. She lay bleeding to death in the courtyard, police said.

Howard Jones, 66, would also die, shot by police who were unable to disarm him.

Friends and neighbors were stunned by the brutal death of Bonnie Jones. They remembered her as a vivacious woman who played the banjo and last year ran the New York Marathon.

“It’s unbelievable,” said friend Paul Watkins, who handled phone calls for the family Monday. “They’re still reeling,” he said.

Douglas Stoltzfus, an upstairs neighbor who rushed to help after hearing Bonnie Jones screaming, said he would never forget the look on Howard Jones’ face.

“It was satanic,” said Stoltzfus.

Police said they had not been called to the apartment for trouble in the past. Stoltzfus, a physician who has lived in the building in the 1100 block of West Pratt Boulevard since 1991, said he never heard fighting coming from the apartment below, but he said others in the building had heard Howard Jones use abusive language with his wife.

When teachers at Clemente heard the news Monday morning, they first felt disbelief and then shock, said Elena Diadenko, an art teacher.

Diadenko said Bonnie Jones worked this year as dean for the senior class, overseeing administrative matters for several hundred students. Much of her day was spent administering discipline, Diadenko said.

“She was sort of like their second mom; someone had to tell them to behave,” Diadenko said, crying. “She was an excellent worker, just excellent,” she said.

Howard Jones had not worked as a doctor since losing his medical license in Iowa in 1993 after being charged with mismanaging anesthetic in four surgeries. Records filed by Iowa medical regulators show he failed to comply with several terms of probation, including undergoing treatment for alcoholism.

Rhys Jones is a noted professional fiddler in the old-time music scene and his parents were active supporters of the Chicago Barn Dance Company, a traditional American dance club popular with old-time music players, according to friends.

Rhys Jones, who was released from St. Francis Hospital in Evanston Sunday, will need surgery to repair a wound to his forearm, said Watkins. Rhys Jones was staying with his father’s brother in Lake Forest and could not be reached for comment.

The bloody scene, which was witnessed by several neighbors, ended a week of trouble for the Jones family. Bonnie Jones called 911 at 10 p.m. on Oct. 10 after her husband punched her in the face, bloodying her nose and giving her a black eye, according to police.

As police were questioning Howard Jones at the apartment, his wife told them “he is gun crazy, he has a gun in the house.” She allowed them to search, and officers found a loaded .357-magnum revolver between the mattresses of the bed, according to the police report.

The next day in court, Howard Jones pleaded guilty and was referred for a mental health evaluation. The judge also granted an order of protection prohibiting him from going to the apartment or having any contact with Bonnie Jones.

Rhys Jones insisted that his mother stay with friends Saturday night, police said. At about 1:30 p.m. Sunday, he accompanied his mother to the family’s apartment just east of Sheridan Road near the lakefront, police said. When they walked up the back steps, they found that a pane of glass in the lower part of the back door was broken out, said Patrick Camden, police spokesman.

They entered the apartment cautiously and found a bedroom door closed, Camden said. When they opened the door, Howard Jones lunged out with two kitchen knives.

The wife and son turned and ran toward the back stairs, Camden said. As they struggled to open the door, Howard Jones slashed and stabbed at them and chased them down the back steps, he said.

Stoltzfus was in his apartment two floors up when he heard “a loud scream that got louder as she called for help.”

Stoltzfus, a family practice physician, rushed down the back steps and came upon the scene in the courtyard.

“Howard was at the base of the stairs, his face streaked with blood, and he was wielding a knife,” he said. Bonnie Jones was lying on the pavement, and her son was trying to fend off the father, and “he was shouting, `Run, Mom. Run, Mom.'”

Stoltzfus picked up a set of burglar bars that had not been installed. He said he swung once at Howard Jones, hitting him on the back of the neck. Another neighbor shoved Jones, knocking him into the wall, before he scrambled back into the apartment, Stoltzfus said.

Bonnie Jones was stabbed many times in the chest and had a large slash wound in her abdomen, Camden said.

When two police officers arrived and went into the apartment, they found Howard Jones sitting on the living room sofa, a bloody kitchen knife in his hands, police said.

“Shoot me, just shoot me,” he said, according to Camden. When police ordered him to drop the knife, he refused and charged the officers. One of them grappled with him for control of the knife.

Seeing his partner losing the struggle, a Rogers Park District sergeant stepped forward and shot Jones in the center of his chest, Camden said.