It could be that Reid has unknowingly crossed paths with a criminal organization. They kidnap him to extract information about the FBI's investigations into their activities. Reid has to endure torture and interrogation, but he also tries to analyze his captors' behavior to find a way to escape.
Well, perhaps a member of the unsub's (the kidnapper's) family or someone close to them has a change of heart. They might contact the BAU secretly and provide information about where Reid is being held. The team could then plan a stealthy operation to get Reid out. Also, Reid is very intelligent. He might be able to manipulate the kidnapper into making a mistake that the BAU can use to their advantage and rescue him.
In many Reid - gets - shot fanfictions, it often focuses on the team's reaction. His friends, like Morgan and Garcia, would be extremely worried. They might rush him to the hospital while trying to keep their emotions in check. The angst and worry would be palpable as they wait for news on his condition.
One possible storyline could be Reid dealing with the shock of an unexpected pregnancy. He might be worried about how it will affect his career in the BAU, as his job involves a lot of physical and mental stress. He could also be concerned about the reactions of his colleagues, especially in a male - dominated field like criminal profiling.
One possible motive could be revenge. Maybe Reid has put away a relative or someone close to the kidnapper in the past. Another motive might be related to Reid's intelligence. The kidnapper could want to use his brainpower for some illegal or self - serving scheme, like cracking a code or coming up with a complex plan.
One great Reid kidnapped fanfiction is 'The Abduction of Reid' on FanFiction.net. It has an interesting plot where Reid is kidnapped by an unsub with a personal vendetta. The author does a great job of building suspense and keeping the characters in - character.
In some fanfictions, JJ could get hurt during a hostage situation. For example, she might try to negotiate with the hostage - taker, but things go wrong and she gets shot. Her injury then becomes a catalyst for the team to work even harder to resolve the situation. Another idea is that she is targeted by a cult because of her work with the BAU. They manage to capture her and inflict harm on her, and the story could revolve around the team's efforts to rescue her and take down the cult. Also, she could be injured in a car accident while chasing a suspect, and the team has to deal with their fear of losing her while also trying to solve the case that led to the accident.
Another theme is Reid's own personal growth during the ordeal. He may face his fears, or learn something new about himself. For example, in some fanfictions, he discovers a new level of strength or resilience that he didn't know he had while being kidnapped.
One scenario could be that Reid gets hurt during a chase. Maybe he trips and falls while running after an unsub, and sprains his ankle. This would slow him down and make him vulnerable.
In some fanfictions, Reid's kidnapping could be related to his family secrets. Maybe there's someone from his past, like a long - lost relative or someone his mother knew, who abducts him to get to something valuable, either information or an object. This could lead to a lot of self - discovery for Reid as he tries to figure out the motives behind his abduction while also trying to escape.
Well, a great fanfiction storyline could involve Reid and Morgan going undercover together. Maybe they have to infiltrate a criminal organization. Reid could use his knowledge of psychology to manipulate the criminals from the inside, while Morgan uses his combat skills to keep them safe. It could also be a story where they are dealing with the aftermath of a traumatic case that has affected them both in different ways, and they help each other heal.