Maybe in some fanfictions, Annabeth could be written as betraying Percy's trust. For example, she might side with his enemies or reveal his secrets, which would deeply wound Percy emotionally.
One possible scenario is that Annabeth might lie to Percy about something really important. For instance, she could lie about her whereabouts when she's actually meeting someone who is not a friend to Percy. When Percy discovers the truth, he would feel betrayed and hurt.
One possible reason could be miscommunication. Maybe Annabeth said something without realizing how it would come across to Percy. For example, if she was stressed about a quest and snapped at him when he was just trying to be helpful.
Annabeth would be very shaken up. After the initial shock, she would assess the situation calmly. If Percy is unconscious, she would try to find a way to wake him up. She might talk to him, recalling their memories together, hoping it would reach him on some level. And she would be very protective of him while he's injured, not allowing any further harm to come to him. She would also feel guilty, thinking that if she were stronger or more careful, Percy wouldn't have had to protect her and get hurt in the first place.
It could be an enemy from the underworld. Maybe a powerful demon or a vengeful spirit that has a grudge against her. They might use their dark powers to harm her, like sending a bolt of dark energy her way.
In a large number of Percy and Annabeth fanfictions, they are indeed presented as soulmates. Their shared adventures, the way they understand each other without many words, and the deep loyalty they have for one another all contribute to this perception. Fanfiction authors often build on their existing relationship from the original works and enhance it to the level of soulmates. They might show it through things like Percy being able to sense Annabeth's distress from afar, or Annabeth always knowing exactly what Percy needs in difficult situations. This soulmate - like relationship makes for very engaging and heart - warming stories in the fanfiction realm.
Maybe they are in a forest filled with dangerous magical creatures. A giant snake - like creature lunges at Annabeth. Percy quickly moves in front of her and the creature bites his leg. In another situation, they are in a magical maze. There are walls closing in on them and spikes starting to protrude from the sides. Percy pushes Annabeth out of the way of a spike that was about to impale her, but he gets scratched all over his body. And they could be in a fight against a powerful sorcerer. The sorcerer casts a spell of dark energy towards Annabeth, and Percy uses his own power to try and block it. However, some of the dark energy seeps through and causes internal damage to Percy.
It could be that Annabeth has a misunderstanding about Percy. She might think he's a threat to her position or status at the camp, so she bullies him to try and keep him in check.
It could be Chiron, the centaur. He's always keeping an eye on the campers and would likely be concerned if he caught them up to something. He might give them a stern talking - to and some extra chores as punishment.
Percy might be a bit flustered and embarrassed. He's protective of his relationship with Annabeth, so having Magnus walk in might make him feel like their privacy has been invaded. He could quickly try to shield Annabeth or just look really shocked.