Protecting what's been hurt in TMNT fanfiction can involve having the other characters show more empathy and understanding. Or, you could introduce a magical element that shields them from further harm. It could also be interesting to have the hurt character discover their inner strength and use it to protect themselves and others.
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.
Raph would be the first to show his concern through anger. He'd be mad at himself for not protecting Leo better and also at the situation that led to Leo's injury. Mikey would be visibly distraught, constantly by Leo's side trying to cheer him up. Donnie would be all business, using his scientific knowledge to figure out the best way to treat Leo's wounds and help him recover.
To effectively write a 'hurt reader' situation in TMNT fanfiction, you need to focus on the emotions. For example, if the reader is physically hurt, describe the pain in detail. Say things like 'The pain shot through the reader's leg like a bolt of lightning, making them cry out in agony.' This makes the reader of the fanfiction feel more connected to the situation.
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.
Splinter, as their sensei and father figure, would offer wisdom and comfort. He might have some traditional methods to help with Donnie's pain and healing. And he would also use this as a teaching moment for all of his sons about the importance of caution and looking out for each other.
Often, there's a moment of self - discovery for Donnie. When he gets hurt, he might realize his own vulnerability and how much he depends on his brothers. This could lead to some emotional moments between them, like heartfelt conversations while he's recovering.
One common scenario could be during a battle with a powerful enemy. For example, the Foot Clan might set up a complex trap and Leo, being the leader, might rush in to protect his brothers and get seriously injured. Another could be in a training accident. Maybe he's trying a new and difficult move and it goes wrong, resulting in an injury.
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.
Raph usually gets really angry. He blames himself for not being there to protect Leo or he gets mad at the enemy who hurt Leo. He'll be the first to want revenge and will be very protective of Leo while he's injured.
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.