Well, it could be that Shadow has some sort of misunderstanding. Maybe he believes Sonic has some information related to a threat to the world. So he kidnaps Sonic to interrogate him. For example, Shadow might think Sonic knows about a new enemy's weakness that Sonic actually doesn't. And Sonic has to convince Shadow of his ignorance while also trying to escape.
It could be Dr. Eggman. He might have manipulated Shadow into kidnapping Sonic. Maybe he promised Shadow something in return, like power - ups for his abilities. Dr. Eggman wants to study Sonic's speed and abilities, so he uses Shadow as a tool to get Sonic in his clutches.
Tails would be the first one to come to Sonic's aid. His intelligence and flying ability would be very useful in finding Sonic and getting past Eggman's defenses.
Well, first of all, it would be a very dark turn for the characters. Amy would likely be terrified, and Sonic would be seen as a villain, which is completely against his heroic nature in the main series. It could also make the readers uncomfortable as it involves non - consensual actions.
In this kind of fanfiction, Sonic might be locked in one of Eggman's elaborate traps. Eggman could be planning to use Sonic's speed for his own evil experiments or to finally defeat him once and for all. Sonic would surely try to escape using his wits and speed.
Another reason is the creativity of the plots. Since it's fan - made, there are no real boundaries. A story could combine elements from different Sonic games or even introduce entirely new concepts. For example, a fanfic could have Shadow and Silver discover a new form of Chaos energy that changes the power balance in their world.
Tails is a very popular character to include. He is Sonic's best friend and his technical skills can add a lot to the story. For example, he could help Sonic and Shadow figure out some complex machinery or technology that is part of the plot.
Sonic would be the first to react. He'd be angry and immediately start the search for Tails. Amy would be worried sick and might try to help Sonic in any way she can, like gathering information from the other animals in the area. Knuckles would be on high alert, thinking this could be part of a bigger plan to get to the chaos emeralds. He'd guard the emeralds even more closely while also keeping an eye out for any signs of Eggman's activities related to Tails' kidnapping.
There may be some fan - made platforms out there that have such fanfiction, but I really don't encourage seeking out content based on this rather dark concept. Sonic and Amy are usually associated with positive themes like friendship and heroism in the official lore.
Yes, there are quite a few out there. Some can be found on popular fanfiction websites. You might need to search through the Sonic the Hedgehog fanfiction section specifically. However, the quality can vary greatly.