It was story time. A pair of 2-year-olds sat on miniature chairs pulled up to a miniature table at Blythedale Children’s Hospital in Valhalla, N.Y., listening attentively.

“We have so many animals that have boo-boos in our book,” a brown-haired woman said in a singsong voice, holding up a book called “All Better!”

“Feel better, doggy,” one of the toddlers, a girl with seven braids, said as she placed a red Band-Aid sticker on the paw of a dog in the book.

The girl, Catherine Arias, was herself recovering from a very real and much more grievous injury. In January 2022, days away from her first birthday, she was caught in the crossfire of a shooting outside a pharmacy in the Bronx. The bullet penetrated the left side of her brain, leaving her with a traumatic injury and weakness on the right side of her body. More than a year and a half later, she still requires five days of therapy every week to improve her ability to eat, talk and move.

Earlier this month, federal prosecutors announced the arrest of two men in connection with Catherine’s shooting, a relief to her parents, who have struggled for months to come to terms with the calamity.

“I just started crying — I couldn’t talk after that,” Gregory Arias, Catherine’s father, said.

“It was like a dry-heave cry,” Miraida Gomez, her mother, said. “The cry that I didn’t get to have processing everything that we’ve been through was the cry that I had that morning.”

The shooting and its aftermath — expensive medical treatment for Catherine, worry over the emotional health of her two older sisters, court appearances for the accused men — have left the family with complicated and conflicting emotions.

Ms. Gomez and Mr. Arias, high school sweethearts, have deep ties to the Bronx, where they were born and raised. They were keenly aware of the violence that can plague their neighborhood. Catherine was one of 56 children shot in the Bronx last year, the highest tally of any part of the city, according to New York Police Department data. Her injury and her long road to recovery are a grim reminder of the life-altering consequences of gun violence across the city, even when shootings are not fatal. Yet Ms. Gomez, a social worker, found herself struggling with something approaching sympathy for the men arrested, wondering what was missing in their childhoods that had led them to the streets.

Still, Catherine’s parents are eager to provide a far better life for their own children and are now saving money to move out of the Bronx — out of the city altogether.

‘I’m seeing death’

On Jan. 19, 2022, Ms. Gomez had finished work and was excitedly planning Catherine’s first birthday party at her mother’s house. She had decided on the theme — pink and purple dinosaurs — and was finishing the guest list and menu.

Her husband arrived to pick her and the baby up after his shift as a delivery driver for an industrial gas company, and they made a quick stop for a prescription at the Leroy Pharmacy on East 198th Street.

“Lock the doors just in case they try to steal me and Catherine,” Ms. Gomez, 34, recalled telling him from the back of the car, where the baby was dozing.

Mr. Arias, 35, went straight to the rear of the pharmacy to retrieve the medication. The store was loud and packed with people wearing masks to protect themselves from Covid-19. He waited in line.

Outside, men were lurking with guns, trying to protect the turf where they were selling cocaine, according to federal prosecutors.

There were one, two, three shots, and then the sound of something hitting the window of the family’s Nissan.

Ms. Gomez had learned from a young age to “stop and drop,” not just for fires but for shootings, too. She went to grab Catherine from her car seat so that they could both hide behind the driver’s seat, but found her baby’s body “full of blood.”

Ms. Gomez unlocked the car and screamed for help. Catherine’s lips turned blue, and Ms. Gomez laid her on the hood of the car and started to give her CPR. A woman gave her a towel and told her to apply pressure to the wound, but Ms. Gomez couldn’t find it. There was blood everywhere, soaking Catherine’s pink jacket.

The bullet had traveled through the back window, the leather seat and Catherine’s car seat, before striking the area between her jaw and skull and traveling up through the left side of her head.

When Mr. Arias returned, he found his wife holding the baby, repeating, “‘It’s OK, baby. It’s OK. It’s OK.” She told him to call 911.

Mr. Arias froze, his fingers hovering over his cellphone but unable to dial.

“I’m seeing her, but I’m not seeing her,” Mr. Arias recalled. “I’m seeing death, I see her passing because she’s not responding.”

‘One too many’

Catherine underwent seven hours of brain surgery. She suffered a seizure and a stroke during the procedure, which led to the hemiparesis, or weakness on the right side of her body.

She spent her first birthday in the hospital: Ms. Gomez placed her party outfit over her body on the hospital bed.

That May, Catherine had titanium mesh implanted on the left side of her skull. In October, the mesh was replaced with a titanium plate, which takes the place of the side of her skull that the bullet shattered.

Catherine still has visual impairment, difficulty swallowing and a number of other medical challenges because of the wound, said Dr. Kathy Silverman, a pediatrician who worked with Catherine for three months.

“The brain is the control center for the body,” Dr. Silverman said. “So it’s not just the brain but every other organ system that you have to keep an eye on when a child comes in with that kind of injury.”

Dr. Silverman, who has worked at the hospital, north of New York City, for more than 20 years, has treated a number of children with gunshot wounds over her career, including children who have shot themselves, those who have been targeted by shooters and those like Catherine, who were caught in the crossfire.

“Having one child with gunshot wounds is one too many,” Dr. Silverman said. “This is a child that needs to be followed over time very closely by a number of physicians, a rehab doctor, a pediatrician, her surgeons, and she needs that intensive rehab to be able to gain the functional skills back.”

“She’s still very young,” Dr. Silverman added.

Cheerios and a climbing wall

For a while, Catherine refused to sit in a car seat.

“I guess maybe she felt the same way she was like when it happened,” Ms. Gomez said, “feeling what she was sitting in at the time, so we had to switch it up.”

Catherine’s car seat is no longer secured to the middle of the back seat as it was the night of the shooting, and is instead buckled in behind the driver’s seat. To the right of the seat, the dent the bullet made can still be seen in the car’s leather interior.

On a recent morning, Ms. Gomez picked Catherine up out of her car seat and carried her into the hospital for therapy. Catherine would spend the next three hours in a program for children with medically complex needs. One young boy wore a yellow backpack that contained feeding tubes. A 3-year-old girl had a tracheotomy to help her breathe.

The classroom was full of natural light streaming in from four skylights. Children squealed and giggled as they played.

“I make a bottle,” Catherine said as she held toy milk up to a doll in a white highchair. “Good job!” the staff called out. “Yay! You did it!”

But the morning wasn’t just for play. Catherine would also undergo dysphagia therapy: exercises to help her eat and drink on her own.

“Which one do you want? Froot Loops or Cheerios?” Gina D. Longarzo, a therapist, asked. Catherine pointed to the heart-shaped Cheerios, kicking her legs under the table.

“We’re going to pour the milk,” Ms. Longarzo said. “Do you want to help Gina?”

The gunshot wound slowed Catherine’s muscles and the timeliness of her swallowing. She initially had a nasal gastric tube before she graduated to eating purée and thick liquids. Now, she’s working on solids, thin liquids and her aversion to food. “Good job, baby!” Ms. Longarzo said as Catherine used her left hand to lift a pink spoon, with her name written on the handle, to her mouth. “Yay!”

“Heart!” Catherine exclaimed, analyzing the contents of her bowl. “Nice heart!”

Catherine had been crawling and standing before the shooting, but the injury set her back. Initially, her physical therapy involved learning again to sit upright and to control her trunk and head without support.

That day, her task in physical therapy was to scale a rock-climbing wall and grab Mickey Mouse heads attached to string, to practice using both sides of her body. In her pink floral Nike sneakers she jumped, climbed and crawled beneath an obstacle course set up near the wall.

“She’s doing really well,” said Brendan Bacon, her physical therapist. He plans to make sure she continues to hit her milestones.

Catherine’s parents are doing their best to make sure she has the treatment she needs. Early on, Ms. Gomez and Mr. Arias exhausted not only the $8,000 they had in savings, but also $30,000 they had received through a GoFundMe campaign that a family member set up for them, largely because they didn’t have health benefits at the time of the shooting; they do now. They said they are still scrambling to make ends meet.

Catherine’s older sisters are in trauma therapy. Haylee, 12, has shut down emotionally, Ms. Gomez said. Seven-year-old Delilah, formerly a star student, has become defiant and uninterested in completing her schoolwork.

‘A miracle’

On Aug. 9, federal authorities announced the arrests of Ahmed Altorei and Samuel Bautista in connection to Catherine’s shooting. Mr. Altorei, 36, and Mr. Bautista, 30, were charged with distributing drugs and carrying guns in connection with a drug trafficking operation, federal prosecutors said in an unsealed indictment.

The U.S. attorney, Damian Williams, called it “a miracle” that Catherine survived the shooting, but said “the emotional and physical trauma will never go away.”

Ms. Gomez and Mr. Arias brought Catherine to the men’s first court appearance. Ms. Gomez said she was surprised to see that they had no family there with them.

“That, to me, shows that perhaps they, as children, found a way to fit in and found love in the streets, which is why they lead those lifestyles,” Ms. Gomez said. She wondered what was missing in their childhoods — and said she initially had the urge to hug them.

One of the men looked remorseful, Ms. Gomez said, but the other seemed to scrutinize her family judgmentally. Whatever fleeting compassion she had was gone.

If the men are convicted, Ms. Gomez, said, she prays that their time in prison teaches them something. For now, the family plans to continue attending the court appearances, and bringing Catherine.

“This little face: That’s going to be your cross to bear every day,” Mr. Arias said.

In the meantime, the family continues to take Catherine to her treatments. They are saving money to move, perhaps to North Carolina. Ms. Gomez said Catherine still gets headaches near where the bullet entered her skull: “She’ll point to the wound, where the bullet went in, and she’ll say, ‘boo-boo, boo-boo.’”