It could also be revenge. Maybe someone who was affected by a past International Rescue mission blames Virgil specifically and wants to make him pay. For example, if a building they owned was accidentally damaged during a rescue, they might target Virgil out of anger.
The motive could be ransom. The kidnappers might know that the Tracy family is wealthy and figure they can get a large sum of money for Virgil's safe return.
One idea could be that Virgil is kidnapped by an old enemy of the Tracy family who wants to use him as bait to get to International Rescue's secrets. Another could be that he's abducted by a group who mistake him for someone else with valuable knowledge. Maybe a mad scientist kidnaps him to force him to help with a dangerous experiment.
One common theme could be the other characters' reactions to Virgil being hurt. For example, how his brothers might step up to support him or take on his responsibilities. Another theme might be Virgil's own struggle to recover and get back to his duties.
Maybe Virgil's injury affects his ability to perform his normal duties in future missions. This could lead to some self - doubt and a struggle to regain his confidence. The other characters would then have to support him both physically and emotionally, like Scott giving him pep talks and helping with his physical therapy.
You can try looking on fanfiction websites like Archive of Our Own (AO3) or FanFiction.net. There are often many different Thunderbirds fanfictions on these platforms, and you can search specifically for ones involving Virgil getting hurt.
His family would be extremely worried. Scott, as the eldest, would likely take charge immediately. He'd be focused on getting Virgil the best medical care possible and coordinating with the rest of the team to ensure his safety.
The motives could be revenge. Somebody who has been wronged by Deidara or the Akatsuki in general might kidnap him to get even. For example, a village that was destroyed by his explosives could seek vengeance.
One possible motive could be to gain power. Since Goten is a Saiyan, his power could be harnessed in some way. For example, they might want to extract his ki or use his DNA for some evil experiment.
Revenge is another motive. Maybe someone has a grudge against the Reagan family for past actions. Nicky is an easy target to get back at them. For example, if the family put someone in jail, that person's accomplice might kidnap Nicky to make them suffer.
One possible motive could be ransom. Maybe some criminals knew that Christian was wealthy and thought they could get a large sum of money for his and Ana's release. Another motive could be revenge. Perhaps someone who had a grudge against Christian or Ana from their past decided to take this extreme measure.
One possible motive could be Bellatrix's loyalty to Voldemort. She might think that by kidnapping Hermione, she can get information about Harry Potter and the Order of the Phoenix. Hermione is known to be very intelligent and Bellatrix could believe she has valuable knowledge. For example, Hermione might know the location of Potter or the Order's plans against Voldemort.