Maybe it's an old foe who has come back with a vengeance. For example, a gem that Steven thought he had defeated before might return and capture him in order to get revenge. This foe could have some new abilities or powers that make it difficult for Steven to escape.
There's also a possibility that it's not a gem but a group of humans. They could be a secret organization that has discovered Steven's powers and wants to study him. They might capture him thinking they can use his powers for some sort of scientific or military advantage.
Well, in this fanfiction, perhaps Steven could be held captive by an old enemy. Maybe he'll have to use his wits to escape, like finding a weakness in the prison's security system.
Maybe a rogue ninja group that wants to sell Naruto to the highest bidder. They see him as a valuable asset due to his strength and status in Konoha.
It could be a rival group. They might be jealous of Serena's abilities or resources and capture her to gain an advantage.
Another option is that it's a human who has somehow discovered the existence of Amethyst and the other Gems. This human could be a mad scientist type who wants to study Amethyst's unique gemstone and abilities. He or she might not understand the full implications of what they're doing and just see Amethyst as an interesting specimen to experiment on.
It could be a new villain that has emerged. This villain might have some sort of vendetta against Steven specifically, perhaps because of his unique powers or his role in the gem world.
Perhaps some remnants of Homeworld's military that still hold a grudge against the Crystal Gems. They might think that by kidnapping Amethyst, they can force the Gems to stop their activities on Earth or give up some valuable information.
Steven would be the main character as he's the one getting poofed. But depending on the context, the Crystal Gems - Garnet, Amethyst, and Pearl - would likely be important characters too. They would probably be involved in the aftermath of Steven getting poofed, either trying to revive him or dealing with the situation his poofing has caused.
Well, 'Steven gets poofed' in a fanfiction could be about Steven from a particular series (like Steven Universe perhaps) facing a situation where he gets poofed, which means he's sort of defeated or incapacitated in some way. It might involve an enemy overpowering him, or a dangerous situation that causes him to be in this state. The fanfiction would then likely explore what happens after, like how his friends react or how he gets restored.
Steven could get hurt while experimenting with his powers. He might push himself too far in an attempt to discover new abilities or to use his existing ones in a more powerful way. This overexertion could lead to him getting physically or mentally hurt. Also, he could be hurt by a Gem who has a vendetta against the Crystal Gems and targets Steven as a way to get back at them.
One common theme is the display of friendship. As Steven is sick, his friends rally around him, showing how much they care. For example, they might all take turns staying by his bedside. Another theme could be self - discovery. Steven might learn more about himself and his limits while being ill. He realizes that he can't always be strong and that it's okay to accept help.