The site is the largest nesting colony of griffon vultures in Israel and home to 40 birds.
The griffon vulture is in danger of extinction, and S-98 was among some chicks sent to the reserve from Spain three years ago so they could be raised and released.
Staff placed an identification ring on its leg, a tag on its wing and a GPS transmitter on its back.
Late last month, the device went silent.
This week, the humanitarian aid organization Israeli Flying Aid contacted the reserve to say that a head of a Syrian rebel militia group had found a bird and sent photos of it.
"They had to check that the vulture was not booby-trapped"
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"I personally raised this vulture, so when I saw the pictures, I was very excited,” Eldad Eitan, a manager at Gamla Nature Reserve, told NBC News.
He said the vulture was lucky to have fallen into the hands of a rebel commander who loved animals and had a particular interest in birds.
Eitan immediately contacted the insurgent to send instructions on how to properly take care of a griffon vulture.
“Usually, vultures eat cow meat, goats and sheep, so that’s what I messaged him,” Eitan said. “He returned the message, saying that [his fighters] didn’t have any meat to eat for themselves, but that he could get chickens.”
The militant said S-98 was fed two chickens a day while his fighters ate only bread.
Eventually, the two men hatched a plan to get the vulture back into Israel.
The commander agreed to bring the vulture back to the Israeli-Syrian border, some 180 miles away from where it was held, in return for humanitarian aid.
“This was a big task for him since he was surrounded by ISIS troops,” Eitan said.
On Thursday, the vulture was handed over to Israeli troops.
“They had to check that the vulture was not booby-trapped and that it was all right,” Eitan added.
S-98 is now back home and is being treated for a leg injury. The bird has been given painkillers and antibiotics, but is in good shape.
After the successful handover, Eitan says he messaged the Syrian commander to personally thank him and express his hope that peace will prevail.
“The Syrians answered me that they, too, hoped that the war will end soon and that they returned the bird as a ‘thank you’ gesture for Israel taking care of wounded Syrians," he said.
They even suggested that they could all meet up one day.
Eitan says the S-98 saga gives him hope for the future.
“The vulture that came back is very symbolic,” he said. “It proves that there is no substitute for humanity.”
Paul Goldman reported from Tel Aviv. Yuliya Talmazan reported from London.
Paul Goldman is a Tel Aviv-based producer and video editor for NBC News.