In some fanfiction, Matt could be kidnapped by a cult - like group that has emerged during the chaos of the alien invasion. They might believe that Matt has some sort of special power or significance due to his association with the resistance. They could be trying to use him to gain power or influence within the new world order. Or perhaps a group of aliens who have a vendetta against Tom Mason (Matt's father) take Matt as a way to get revenge on Tom.
Maybe in the fanfiction, Matt is kidnapped by an unknown alien faction that has just arrived on Earth. This new group might not be aware of the complex relationships on Earth and simply take Matt because he was in the wrong place at the wrong time. They could be studying humans and think Matt is a good specimen to start with. Also, it could be that a group of desperate survivors, in need of supplies, kidnap Matt thinking they can trade him for what they need from the main group in 'Falling Skies'.
One possible scenario could be that Nightwing is kidnapped by a new supervillain who wants to use him as bait to lure Batman. The villain might hold Nightwing in an abandoned warehouse, setting up various traps. Another could be that a criminal organization kidnaps him to extract information about the other heroes in Gotham. They might use high - tech devices to try and break his will.
Well, it could be that Clarke is kidnapped by a group who wants to use her knowledge for some devious plan. Bellamy, being her closest ally, uses his tracking skills to find her. He might also discover some secrets about Clarke's past during the rescue journey. And along the way, their relationship could deepen even more.
As mentioned before, it could be rogue skitters. They are often portrayed as a threat in the show, and kidnapping Matt would be a strategic move for them.
It could be that a long - time nemesis of Jane finally gets the upper hand. This nemesis has been planning for a long time, waiting for the perfect moment to strike. They manage to ambush Jane when he's alone and vulnerable, shooting him and leaving him for dead. But of course, Jane's tenacity and the team's determination would lead to an interesting recovery and revenge plot.
One possible plot could be that Ash is kidnapped by a rival trainer group who want to steal his Pokémon. His friends then have to embark on a rescue mission, facing various challenges and battles along the way.
In some 'goku gets hurt fanfiction', he might get hurt while protecting his friends or family. For example, he could take a fatal blow meant for someone else. This would not only physically harm him but also add an emotional aspect to the story as his loved ones would be worried and try to save him.
In the fanfiction, perhaps Loki's sickness is a result of some magical backlash. As he gets sicker, he could start having strange visions or nightmares that are related to his past misdeeds. His loyal followers might then try to find a cure for him, leading to an adventure to seek out a powerful healer.
Well, in some fanfictions of this kind, Naruto could be tortured physically by being chained up and beaten. His captors might also starve him or deprive him of water to weaken him. It could also be that they use some sort of dark magic or forbidden techniques on him that cause extreme pain and discomfort.
Well, perhaps in the fanfiction, Goku gets mad when he discovers that someone has been using his name for evil deeds. This would go against his values of justice and protecting the innocent. He might get really angry and go on a search to clear his name and stop the impostor. Or it could be that a new, extremely powerful villain emerges and starts to destroy planets without any remorse. Goku, being the defender of the universe, would be enraged by such senseless destruction and would confront the villain with all his might.
One possible scenario could be that he is killed in a lightsaber duel by a powerful Sith opponent. Maybe this new Sith has some secret technique that Anakin couldn't counter.