One possible storyline could be that a villain manages to impale a hero during a battle. For example, a powerful meta - human villain with sharp - edged weapons as part of their powers could catch the Flash off - guard and impale him. This could lead to a story of the Flash's struggle to recover, both physically and mentally, and his allies' efforts to protect him while he heals.
I'm not sure of specific fanfictions with that exact scenario off - hand. You could try searching on popular fanfiction websites like Archive of Our Own. Just type in 'The Flash impaled hurt' in the search bar and see what comes up.
In this fanfiction, it might be that an enemy has found a way to manipulate the Speed Force to harm the Flash. For example, they could be using some sort of device that alters the nature of the Speed Force in the Flash's vicinity. So, the Flash has to not only deal with the pain but also figure out who is behind this and stop them before the damage becomes irreversible.
Maybe Jack gets hurt while trying to protect someone in the dojo. This could lead to a story where he has to deal with his injury while also facing the person or situation that caused the danger in the first place. His sensei could play an important role in guiding him through this difficult time.
One possible storyline could be them dealing with the initial shock and then preparing for the new arrival. They might face challenges from their superhero duties while also getting ready to be parents. For example, they could be worried about how to keep their child safe in a world full of villains.
Maybe Kendall is exploring an ancient Dino Charge related site on her own for some important research. However, she accidentally triggers a hidden trap. She gets hurt, and the Rangers have to find her in the dangerous site while also dealing with the fact that she's injured and needs immediate medical attention. This could add a lot of tension to the story.
One possible storyline could be that Amy gets hurt while trying to protect Sonic from an enemy. Maybe she jumps in front of a powerful attack meant for Sonic. Another could be that she gets injured during a dangerous adventure in a new, uncharted zone. For example, she might fall into a hidden trap.
One possible storyline could be that Morty gets hurt during one of their inter - dimensional adventures. Maybe they land on a planet with dangerous wildlife and Morty is attacked while Rick is distracted trying to fix the portal gun. Another could be that Morty gets injured in a fight with one of Rick's enemies who target Morty to get back at Rick. It could also be that Morty gets hurt due to his own clumsiness while handling some of Rick's wacky inventions in the garage.
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.
Well, perhaps Spiderman is poisoned by a new type of toxin from a villain. The Avengers then scramble to find an antidote. Black Widow uses her espionage skills to track down the origin of the toxin, while Hulk, in his Banner form, tries to analyze it scientifically. Thor might also use his Asgardian knowledge to see if there are any magical cures. In the meantime, they keep Spiderman comfortable and safe from further attacks.
A great storyline could be about a mystery that spans both their cities. They start investigating separately but soon realize they need each other's help. Team Arrow has the skills to infiltrate dangerous locations, while Team Flash can quickly travel between the two cities to gather information. There could also be a storyline where a powerful and ancient artifact is discovered, and both teams want to keep it safe from falling into the wrong hands. They would need to overcome their differences in approach to protect the artifact and the world from its potential misuse.