In some fanfics, Natasha might get physically hurt during a mission because the other Avengers misjudge a situation. For example, they might not provide the backup she needs in time, and she ends up getting seriously injured. This not only causes her physical pain but also emotional distress as she realizes she can't fully rely on her team.
Another possibility is that the Avengers are under some sort of mind control and end up attacking Natasha. She has to fight back against her friends, which is extremely painful for her. It's a situation where she is caught between self - defense and not wanting to harm those she cares about.
One scenario could be Captain America getting seriously injured during a battle that the Avengers underestimated. He might be left alone and struggling against a powerful enemy, which makes fans feel sad for his pain and isolation.
Another situation could be Jungkook getting physically hurt during a travel accident. His fans and the members would be worried sick. The fanfic might then focus on his recovery process, how he struggles with physical therapy, and the love and support he receives from everyone around him.
One scenario could be Reid getting kidnapped by an unsub. The unsub might torture him physically and psychologically, like depriving him of sleep and constantly taunting him about his past traumas. This would be really painful for Reid and make for a very angsty fanfic.
One possible scenario could be Deidara getting seriously injured during a battle with a powerful enemy. Maybe he underestimates his opponent and ends up with life - threatening wounds. His comrades might be too far away to help immediately, leaving him to struggle alone.
One scenario could be Hiccup getting seriously injured during a dragon fight. Maybe he's protecting Toothless and takes a direct hit from another dragon's attack. This could lead to a story of his slow recovery, with his friends and family rallying around him.
One scenario could be Naruto being forced to choose between the safety of the village and Boruto's life in a dangerous situation. Maybe he has to send Boruto on a near - impossible mission for the greater good, which really hurts Boruto as he feels abandoned by his father. Another could be Naruto being under a genjutsu and unknowingly attacking Boruto, causing physical and emotional harm.
One scenario could be Minho getting seriously injured during a dangerous maze run. Maybe he gets attacked by a griever and sustains deep wounds. His friends would then be in a panic, trying to get him back to safety while also fearing the worst for him.
Another possibility is that Troy is hurt in an accident outside of his Power Ranger duties. This forces him to deal with his vulnerability and the fear that he might not be able to return to his role as a Power Ranger. His friends then have to support him through his recovery both physically and mentally.
Writers can use detailed descriptions of Natasha's pain. For example, if she's been physically injured, describe how she struggles to stand, the look of agony on her face. This makes the readers feel more empathetic towards her.
There are also fanfictions where Arya is betrayed by someone she thought was a friend. This is a very hurtful situation for her as she has always been cautious about who to trust. When this trust is broken, it can lead to a downward spiral of emotions for her, and it makes for a very emotional read for the fans.