It could also be for power. Some evil shinobi might believe that by capturing Naruto and somehow extracting the Nine - Tails' power, they can become extremely powerful. They might have some sort of dark jutsu or experiment in mind that requires the power of the Nine - Tails which is sealed within Naruto.
Another motive could be revenge. Maybe some in Iwa still hold grudges against Konoha for past conflicts. Since Naruto is a prominent figure in Konoha, kidnapping him would be a way to strike back at the village. They might think that by harming Naruto, they can make Konoha suffer.
Well, Obito could be doing it out of revenge. He has a long - standing grudge against the Hidden Leaf Village. Naruto is seen as a symbol of hope in the village. So, by kidnapping him, Obito could be trying to strike a major blow to the village's morale and show that their so - called 'hope' can be easily taken away.
Perhaps in the fanfiction, there is a prophecy or a vision that Tsunade has seen which makes her think that Naruto needs to be in a certain place or situation for the greater good. And she is so desperate to fulfill this that she resorts to kidnapping Naruto. This could lead to a story where Naruto initially resists but then comes to understand Tsunade's reasons as the story progresses.
One possible motive could be to gain control over Naruto's power. Since Naruto has the Nine - Tails within him, Danzo might want to use that power for his own political or military gains. He's always been power - hungry and sees Naruto as a tool to achieve his goals of making Konoha stronger in his own way, which might involve more underhanded and controlling methods.
One possible motive could be power. Danzo was always obsessed with having power in Konoha. By experimenting on Naruto, who is the Jinchuriki of the Nine - Tails, he might have hoped to harness the power of the Tailed Beast in some way. Maybe he thought he could create a super - soldier or gain some unique abilities from Naruto's connection to the Nine - Tails.
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.
Perhaps in this fanfiction, Dumbledore has a secret plan related to Harry's power. He might think that by kidnapping Harry, he can train him in isolation to fully develop his magical abilities without the distractions and potential dangers at Hogwarts. It could also be that Dumbledore is trying to hide Harry from Voldemort in a way that no one would suspect, as Voldemort would never think Dumbledore would use such extreme measures against Harry.
One possible motive could be money. The Stark family is wealthy, so the kidnappers might be after a large ransom. They could think that by holding Peter captive, they can force Tony Stark to pay up a huge sum.
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.
Perhaps in the fanfiction world, Naruto has lost his sanity for some reason. Maybe he has been through a traumatic event that has warped his sense of right and wrong. Hinata, being someone he cares about deeply, becomes a target of his deranged actions. However, this would be a very dark take on the Naruto - Hinata relationship, and often such fanfictions use this extreme situation to then explore how Hinata might be able to bring Naruto back to his senses, or how the other characters in the Naruto universe would react to such a situation.