One possible plot could be that Tobi kidnaps Kakashi to gain some valuable information. Maybe he wants to know about the Sharingan secrets Kakashi has. Tobi could hold Kakashi in a secret lair and try to interrogate him.
Naruto would probably be one of the first to try and rescue Kakashi. He has a strong bond with Kakashi and would not stand by while his teacher is in danger.
In this fanfiction, perhaps Kakashi and Tobi meet in a battle. Kakashi might initially be suspicious of Tobi's true identity. Tobi could be playing mind games with Kakashi, trying to throw him off his game.
Well, one possibility could be that Itachi has some hidden motive related to the Uchiha clan's secrets. He might think Kakashi knows something crucial. So, he kidnaps him to interrogate him in a secret location.
Kakashi could use his Sharingan to analyze Obito's moves and find a weakness in his defenses. Since he has the Sharingan, he might be able to predict Obito's attacks and counter them effectively, eventually finding an opportunity to break free.
Kakashi could become more distrustful after meeting Tobi. Since Tobi is such a mysterious figure, Kakashi might start to suspect everyone around him more.
Naruto would likely be involved. He has a strong bond with Kakashi and would surely try to rescue him. Sasuke could also be part of the story. Given his relationship with Itachi, it would add an interesting dynamic.
Well, perhaps Kevin kidnaps Gwen because he wants to use her as a bargaining chip against Ben. He might think that by having Gwen in his control, he can force Ben to give up the Omnitrix or something valuable. Another possibility is that Kevin has some sort of grudge against Gwen specifically, maybe related to her magical powers that he either fears or envies.
One possible plot could be that Sasuke has some misunderstanding. He might think Naruko is in danger from some hidden enemy in the village. So, he kidnaps her to protect her, but Naruko doesn't understand his intentions at first and struggles against him. Eventually, they start to communicate and Sasuke explains his reasons.
Well, in this kind of fanfiction, perhaps Bowser kidnaps Peach because he wants to make her his queen. Peach, being the strong - willed character she is, tries to escape on her own while Mario is on his way. Bowser sets up all sorts of traps to keep Mario from reaching Peach. The fanfiction could also explore the relationship between Bowser and his minions during this time, like how they take care of Peach while she's captive.
Perhaps in the fanfiction, Madara kidnaps Sakura because he realizes her potential as a medic - nin. He wants her to heal his old wounds or maybe study her unique healing abilities to find a way to make himself invincible. He could keep her in a hidden lair and force her to perform medical experiments on him.