Making a nerve-wracking 3,000-mile journey from Ukraine, into Russia-occupied territory, and back again, a group of mothers managed to recover their children from the custody of the Russian authorities.

For weeks after Russian troops forcibly removed Natalya Zhornyk’s teenage son from his school last fall, she had no idea where he was or what had happened to him.

Then came a phone call.

“Mom, come and get me,” said her son, Artem, 15. He had remembered his mother’s phone number and borrowed the school director’s cellphone.

Ms. Zhornyk made him a promise: “When the fighting calms down, I will come.”

Artem and a dozen schoolmates had been loaded up by Russian troops and transferred to a school farther inside Russian-occupied Ukraine.

While Ms. Zhornyk was relieved to know where he was being held, reaching him would not be easy. They were now on different sides of the front line of a full-blown war, and border crossings from Ukraine into Russian-occupied territory were closed.

But months later, when a neighbor brought back one of her son’s schoolmates, she learned about a charity that was helping mothers bring their children home.

Since it is illegal for men of military age to leave Ukraine now, in March Ms. Zhornyk and a group of women assisted by Save Ukraine completed a nerve-wracking, 3,000-mile journey through Poland, Belarus and Russia to gain entry to Russian-occupied territory in eastern Ukraine and Crimea to retrieve Artem and 15 other children.

Then they had to take another circuitous journey back. “Come on, come on,” urged Ms. Zhornyk, as a cluster of children, laden with bags and suitcases, emerged hesitantly through the barriers at a border crossing from Belarus into Ukraine. She had crossed with her son just hours earlier and pushed forward impatiently to embrace the next group.

“There are no words for all the emotions,” Ms. Zhornyk, 31, said, describing her reunion with Artem. “I was full of emotion, and nervous, nervous.”

In the 13 months since the invasion, thousands of Ukrainian children have been displaced, moved or forcibly transferred to camps or institutions in Russia or Russian-controlled territory, in what Ukraine and rights advocates have condemned as war crimes.

The fate of those children has become a desperate tug of war between Ukraine and Russia, and formed the basis of an arrest warrant issued last month by the International Criminal Court accusing President Vladimir V. Putin of Russia and Maria Lvova-Belova, his commissioner for children’s rights, of illegally transferring them.

Once under Russian control, the children are subject to re-education, fostering and adoption by Russian families — practices that have touched a particular nerve even amid the carnage that has killed and displaced so many Ukrainians.

Ukrainian officials and human rights organizations have described these forced removals as a plan to steal a generation of Ukraine’s youth, turning them into loyal Russian citizens and eradicating Ukrainian culture to the point of committing genocide.

Months of Fear and Anxiety

No one knows the full number of Ukrainian children who have been transferred to Russia or Russian-occupied Ukraine. The Ukrainian government has identified more than 19,000 children that it says have been forcibly transferred or deported, but those working on the issue say the real number is closer to 150,000.

Russia has defended its transfer of the children as a humanitarian effort to rescue them from the war zone, but it has refused to cooperate with Kyiv or international organizations in tracing many of them. After the I.C.C. issued the arrest warrant for Ms. Lvova-Belova, she said that relatives were free to come and collect their children but that only 59 were waiting to go home — a claim that Ukrainian officials have dismissed as absurd.

For the thousands of children who have been transferred, some from broken homes and disadvantaged families, being away from home so long has been an ordeal. Some are in tears when they call home and cannot speak freely, their parents said.

The parents, already living through the trials of Russian occupation, displacement and bombardment, have had to endure months of anxiety, fearful that their children will be sent farther away or given up for adoption in Russia.

And then there is the guilt. Some sent their children to summer camps in the Crimean peninsula, having been assured they would return in two weeks. Others simply yielded to pressure from officials and soldiers to let their children be taken. They all blamed themselves when they were not returned.

“I felt completely lost, I gnawed away at myself,” said Yulia Radzevilova, who brought her son, Maksym Marchenko, 12, home in March after he spent five months in a camp in Crimea. “No one supported me. Family, parents, friends started accusing me.”

But other children were transferred without warning or, like Artem, just disappeared.

Artem had traveled to his school in Kupiansk on Sept. 7 — just as Ukrainian troops were driving out Russia’s occupation — to retrieve documents he needed for college. No bus returned that day, so he remained overnight. The next day, Russian troops turned up and loaded him and other students into military trucks.

“They were Russian,” Artem said in an interview. “In camouflage, with Kalashnikovs.” He thought of fleeing over the back wall of the school, he said, but the teachers made sure all the children climbed on board.

When he did not return home, his mother tried to go to Kupiansk to find him, but turned back under heavy shelling. For three weeks there was no electricity or phone service in her village because of the fighting. With no word of his whereabouts, she registered him as missing with the police.

Then came Artem’s phone call. He said that he and his schoolmates, aged 7 to 17, had been taken to the town of Perevalsk, in Russian-occupied eastern Ukraine, where they were left in a boarding school.

He was only a few hours away by car but in territory closed off by the war.

“It was hard,” she said, shaking her head, “very hard.”

Searching for a Child With Autism

Across the country in southern Ukraine, Olha Mazur faced an even more daunting search. Her son, Oleksandr Chugunov, 16 — Sasha for short — lived in a residential school for disabled children in Oleshky, across the Dnipro River from the city of Kherson where she lived. Sasha is autistic, and cannot talk, she said.

She last saw her son in the summer. Kherson was still occupied and a Russian director had been placed in charge of his school. Then the bridge across the Dnipro was bombed and she could no longer travel to see him. In November, she saw a list online naming him among children transferred to Crimea by the Russians.

She was relieved and worried at the same time. “I am grateful that he is alive,” she said, but the school never informed her what they were doing, and Sasha had no way to communicate with her.

Parents of children in a variety of summer camps and schools began learning through phone calls with their children that the schools would let them go home, but only if their parents came to collect them in person.

Few, if any, of the mothers had the wherewithal to manage such a trek. But there are several charity groups helping to do just that, and Ms. Zhornyk had heard about one, Save Ukraine.

Founded after Russian forces attacked in 2014, the group was created to move children and their families from occupied areas and places of intense fighting to shelters or new homes. After children became stranded in Russian-occupied territory last fall, the group began to organize rescue missions. The mothers set off on that 3,000-mile journey through Poland, Belarus and Russia and on to Russian-occupied Ukraine and Crimea.

They had to navigate hostile border and police checks along the route, which included a flight from Belarus to Moscow, including nine hours of questioning from immigration officers at the airport. From Moscow they drove more than 1,000 miles to Crimea. Ms. Zhornyk split off to go to Perevalsk for Artem. Then the whole group traveled back the way they came, and back into Ukraine through Belarus.

A Debilitating Experience

There were hugs and tears when the mothers and children arrived back in Ukraine last month. And some surprises.

The children were full of stories that went unsaid in phone calls home. Many of the teenagers were able to make daily calls home. Others, like Artem, had to beg to borrow someone’s phone. There were frequent punishments, as well as pressure to sing the Russian anthem, bullying and name-calling by other students, the children said.

There was also mounting stress: The children were told that if their parents did not collect them by this month, six months after their arrival, they would be sent to foster homes or put up for adoption.

“He no longer had any hope that I would come,” Ms. Radzevilova said of her son. “Because I said I didn’t know how, I didn’t have the money.”

Ms. Mazur was even more critical of Russian behavior. Her autistic son had deteriorated in the time they were separated, she said.

“He was never like this,” she said. “When he leaves the car, he is afraid of everything.”

She worried for the other disabled children from Sasha’s original care home in Oleshky, some of whom were wheelchair-bound or bedridden. There was no record of where they went, she said, and she was haunted by the comment of a Russian administrator who told her the Ukrainian children had been cast away “like kittens.”

Of the 13 evacuated from the Kupiansk boarding school last September, only two have returned to Ukraine, including Artem. Another went to Poland. Four children moved to somewhere in Russia, possibly with their parents. Five children remained at the school in Perevalsk, including two girls in first grade. They were in class when Ms. Zhornyk collected her son; he left without saying goodbye.