In the fanfiction, it could be that Naruto is crying because of a lost loved one. Sakura, upon seeing him, is filled with empathy. She sits beside him and they share memories of the person. This shared moment of grief brings them closer together. Sakura might then vow to always be there for Naruto in his times of sorrow, and Naruto realizes how important Sakura's friendship is to him.
Maybe Naruto is crying over a failed mission where he blames himself for the outcome. Sakura sees him and at first is shocked as Naruto is usually so strong. She then consoles him, reminding him of all the times he has succeeded and how this one failure doesn't define him. This could lead to a growth in their relationship where Naruto starts to see Sakura as more than just a teammate.
One possible plotline could be that Naruto punches Sakura out of anger during an argument over Sasuke. Maybe Sakura is being too pushy about bringing Sasuke back in a way that Naruto doesn't agree with, and in a moment of frustration, Naruto lashes out. Another could be that Naruto is under some sort of mind - control and doesn't recognize Sakura, leading to him punching her. It could also be a sparring session gone wrong where Naruto misjudges his strength and accidentally punches Sakura hard.
Perhaps Shikamaru has made a decision that deeply affects Naruto. For example, Shikamaru might choose to leave the village for a dangerous solo mission. Naruto, who values their friendship, cries because he's worried about Shikamaru's safety and the thought of losing his friend. In the fanfic, this could lead to Naruto trying to convince Shikamaru to change his mind.
Perhaps Naruto dies in a fight against a long - hidden evil within the ninja world. Sakura's tears could be a symbol of the end of an era. In the fanfiction, she could struggle with guilt, thinking she could have done more to prevent his death. She may also find strength in her grief and become a more determined ninja, vowing to protect the world Naruto gave his life for.
One possible fanfiction could be that Kakashi stumbles upon Naruto crying alone in the forest. He sits beside Naruto quietly, not saying a word at first. Then he gently puts his hand on Naruto's shoulder and tells him that it's okay to cry, that showing vulnerability doesn't make him weak. Naruto then pours out his heart about his loneliness and how much he misses his parents. Kakashi listens intently and shares some of his own experiences of loss, creating a deep bond between them in that moment.
One possible plotline could be her life before having Sakura. Maybe she was a kunoichi herself and had her own adventures in the Hidden Leaf Village.
A plot could be that Orochimaru, seeking redemption in a way, starts to train Sakura in some unique and dark arts that he has mastered. Sakura, with her determination to become stronger, accepts this training but struggles with the moral implications. This could lead to an internal conflict within her as she tries to balance her new - found power with her values. Another possibility is that Orochimaru places a curse on Sakura for some reason, and she has to find a way to break it. In her quest to break the curse, she delves deeper into Orochimaru's lair and discovers more about his true motives and plans. Or perhaps Orochimaru kidnaps Sakura to use her as a bargaining chip against Sasuke. But Sakura uses her wits and ninja skills to not only escape but also turn the tables on Orochimaru, showing him that she is not to be underestimated.
Perhaps in the fanfiction, Sakura has been poisoned or affected by a strange jutsu that makes her lose control of her emotions and physical actions. This could lead to her lashing out at Naruto and injuring him. Or it could be that Sakura is in a desperate situation where she believes sacrificing Naruto is the only way to save the greater good. So, she makes a tough decision and injures him in the process. It could also be a part of a training exercise gone wrong. They could be training together and Sakura accidentally uses too much force or a new technique she hasn't fully mastered yet, resulting in Naruto getting injured.
One possible plotline could be that they discover their relation and then Naruto becomes overprotective of Sakura. Another could be that they have to face some family secrets together. Maybe there's a hidden power in their family that only they can unlock as siblings.
One possible plotline could be that Sakura realizes her feelings for both Naruto and Sasuke are more than just friendship. She might become possessive out of fear of losing them. For example, she could try to keep them from going on dangerous missions alone. Another could be in a post - war scenario where she sees other people getting close to Naruto and Sasuke and her possessiveness kicks in as she has been through so much with them. She might start small, like being extra clingy, and then it could develop into more complex relationship dynamics as the story progresses.
In the fanfic, it might be set in an alternate universe where Sakura has a different personality. She could be more aggressive and competitive with Naruto. During a sparring match, she goes too far and seriously hurts Naruto. This could then be the starting point of a story about Naruto having to forgive her and them rebuilding their friendship.