Maybe Spike tries to prove himself by joining in on a dangerous adventure with the Mane 6. They are exploring an old, abandoned castle filled with traps. Spike, being smaller and not as experienced as the others, steps on a pressure - sensitive tile that releases a volley of arrows. He gets hurt as some of the arrows graze his body, and then the group has to figure out how to treat his wounds while still making their way through the dangerous castle.
In a fanfiction, Spike could get hurt while trying to protect one of his friends. Let's say Rainbow Dash is being chased by a group of mean - spirited pegasi from another town. Spike jumps in front of Rainbow Dash to shield her from a magic attack they were about to launch. The attack hits Spike hard, and he is left with a large gash on his side. This then leads to a story about how the Mane 6 and all of Ponyville come together to help Spike recover and also deal with the unfriendly pegasi.
One possible storyline could be Spike discovers a long - lost magic spell that is connected to Celestia's past. He embarks on a journey to find out more about it and ends up having to team up with Celestia. Along the way, they face various challenges and learn more about each other's strengths and weaknesses.
One possible storyline could be that Shikadai is on a mission and gets caught in an unexpected ambush by a group of powerful enemies. He might be outnumbered and sustain injuries while trying to fight them off and protect his comrades. Another could be that he's involved in a training accident that goes horribly wrong, like a jutsu backfiring on him and causing him physical harm.
One possible storyline could be that Spike's death has a profound impact on Twilight Sparkle, leading her into a deep depression. She might struggle to carry on with her studies and magic without his constant support.
In a more complex storyline, Evan could get hurt as a result of some sort of conspiracy against the medical practice. Maybe someone is trying to sabotage the hospital and they target Evan as he is often involved in the administrative side. They set up a situation where he is exposed to a harmful substance or gets physically attacked, which then leads to a long journey of recovery and uncovering the truth behind the attack.
In some fanfictions, JJ could get hurt during a hostage situation. For example, she might try to negotiate with the hostage - taker, but things go wrong and she gets shot. Her injury then becomes a catalyst for the team to work even harder to resolve the situation. Another idea is that she is targeted by a cult because of her work with the BAU. They manage to capture her and inflict harm on her, and the story could revolve around the team's efforts to rescue her and take down the cult. Also, she could be injured in a car accident while chasing a suspect, and the team has to deal with their fear of losing her while also trying to solve the case that led to the accident.
Maybe Nightwing is trying to protect a civilian in front of his brothers. He jumps in front of a dangerous weapon aimed at the civilian. The weapon is some sort of experimental tech that causes a lot of internal damage. His brothers witness this selfless act and it stirs up a mix of emotions - pride in his heroism but also anger towards the attacker. They then have to deal with not only getting Nightwing medical attention but also hunting down the perpetrator.
One possible storyline could be that they are on a case and get caught in a trap set by the unsub. For example, they might be lured into an abandoned building where the unsub has rigged it to collapse. JJ could get trapped under some rubble while trying to protect Penelope. Another could be that they are poisoned during an investigation. Maybe they accept food or drinks from someone connected to the case who has ulterior motives. Penelope might be the first to show symptoms, and JJ is desperately trying to find a cure while also dealing with her own growing illness from the poison.
In some fanfictions, Sasuke might get hurt by a curse that was placed on him long ago. As he suffers, he has visions of his past, his family, and his mistakes. His struggle with the physical pain and the emotional turmoil of his past makes for a very engaging and complex storyline.
In a story, there could be a situation where a magical curse is spreading. Beast Boy, seeing Raven in the path of the curse, uses his own body to block it. As a result, he is infected by the curse which starts to harm him physically and mentally. Raven then embarks on a journey to find a cure, all the while taking care of Beast Boy and their relationship deepens through this difficult time.
It could be that Spike is kidnapped by a new, unknown threat from outside of Equestria. This new enemy might see Spike as a key to unlocking some sort of powerful magic in Equestria. Pinkie Pie could use her intuition to find out where Spike is, while Rarity might use her connections to get information on this new enemy.