One possible plotline could be that Tails is killed by a powerful enemy during a battle to protect his friends. Maybe a new, extremely strong villain emerges and Tails sacrifices himself to buy Sonic and the others time to escape. Another could be that there is some sort of accident in Tails' workshop while he is working on a dangerous experiment, leading to his untimely death. It could also be that in a dark alternate universe, Tails is targeted and assassinated by an evil organization that wants to disrupt the balance of power in the world he lives in.
Sonic would be devastated. He and Tails are like brothers. Sonic would likely go into a rage and vow to avenge Tails' death. He would immediately start hunting down whoever or whatever was responsible. Amy would be heartbroken as well. She would probably be the one to try to comfort Sonic while also being deeply sad herself. Knuckles would be angry and ready to fight alongside Sonic to seek justice for Tails.
Often, there could be a theme of adjustment. Tails having to adjust to his new, larger body. This could involve things like how he moves around, his confidence levels, and how he interacts with the world around him. It might also touch on themes of body image, as he might struggle with how he looks now that he's fat. There could also be a sense of adventure where he has to overcome new challenges because of his size, like fitting through small spaces or being slower in movement.
One possible scenario in this fanfiction could be that Naruto gains the Juubi Ten - Tails Eye and his power skyrockets. He might use this newfound power to protect the Hidden Leaf Village from even greater threats. Maybe he could even use it to bring about a new era of peace in the ninja world, as his already strong will and determination would be enhanced by the power of the eye.
One common theme is the rescue mission. The friends of Tails will usually band together to save him. For example, Sonic will use his speed to find out where Tails is held and then they will all figure out a plan to break him out.
One possible plot could be that Tails is captured by an evil scientist. The scientist then roboticizes him against his will. Tails has to struggle to keep his original self and memories while being forced to do the scientist's bidding. Eventually, he might break free from the robotic control through the power of friendship with Sonic and the others.
It could be a new villain who has heard about Tails' mechanical skills. This new baddie might think that by kidnapping Tails, they can force him to build powerful weapons for them.
In such a fanfiction, Tails might be kidnapped by an old enemy like Dr. Eggman. His friends, like Sonic, would then start a rescue mission. They would search all over the place, from the Green Hill Zone to Eggman's secret bases.
Another plot could involve Tails trying to hide his sickness at first because he doesn't want to worry his friends. But as it gets worse, he can't hide it anymore. His friends then feel guilty for not noticing earlier and they all come together to take care of him and find a remedy.