In a fanfiction, Mikey might get hurt during a mission to infiltrate a Kraang base. He could be detected by security systems and get zapped by some sort of electric defense mechanism. This would leave him weak and in pain. His brothers would need to carry him out of there and find a way to reverse the effects of the zap. They'd be desperate to get Mikey back to his normal, energetic self.
In many 'TMNT Mikey hurt' fanfictions, a common plot element is Mikey's own attitude towards his injury. Sometimes he tries to be brave and not show how much pain he's in to not worry his brothers. Another element is the search for a cure or solution. If he's poisoned, they'll look for an antidote. If it's a physical wound, they'll try to find medical supplies or a way to heal it. And there's usually a lot of brotherly bonding as they take care of Mikey.
Leo would likely take charge immediately. He'd assess the situation and start giving orders on how to help Mikey. He'd be calm on the outside but worried on the inside.
Well, his brothers would probably go on a wild rescue mission. They'd search every nook and cranny of the city. Maybe they'd get some help from April and Casey too.
In this fanfiction, Mikey might gain new and unexpected powers. Maybe he could develop the ability to control certain elements like water or fire, which would add a whole new dynamic to his character and the story.
Leo would probably take charge immediately. He'd be focused on getting Mikey to safety and finding a way to treat his injuries. He might be blaming himself a bit for not being there to protect Mikey better.
One possible scenario could be that Mikey gets hurt during a fight with the Foot Clan. Maybe he underestimated an opponent and got a nasty cut on his arm. His brothers would then rush to his side, with Donnie trying to patch him up as quickly as possible while Leo and Raph stand guard, ready to fend off any further attacks.
April and Casey might also be part of this fanfiction. April could use her reporting skills to try and figure out what's going on with Mikey's mutation, and Casey would be ready to fight any new threats that come along because of Mikey's changed state. Also, Splinter, as their sensei, would be guiding them all through this difficult time, providing wisdom and training to help Mikey control his new powers if he has any.
It could be Shredder. He's always been after the turtles.
One possible plot twist could be that Mikey was kidnapped by an unexpected enemy, like a former ally who turned bad. Maybe it was someone he trusted, and this betrayal adds a layer of drama.
In a fanfiction, Mikey might get hurt while trying to protect his brothers. For example, if the Kraang were attacking and his brothers were in danger, Mikey could jump in front of a powerful blast meant for them. This would leave him seriously injured, with his brothers then having to take care of him and find a way to heal him.