He may become angry. Percy has a bit of a temper, so he could lash out at the situation or even at Annabeth if she's still around. He might feel betrayed and start to question all the things they've been through together. He could also go into a state of depression. Losing Annabeth, who has been such an important part of his life, could make him withdraw from his friends and activities. He may lose his motivation for quests and just mope around, feeling sorry for himself.
Percy is likely to be heartbroken. He may initially be in a state of shock, not being able to believe that Annabeth has left him and their daughter. He might feel angry as well, feeling betrayed by her sudden departure.
One possible reason could be that she might be facing some sort of internal conflict. Maybe she has some unresolved issues from her past that resurface and make her feel like she can't be a part of Percy and their daughter's life. It could also be that she feels pressured by some external force, like a new threat in the world of the fanfiction that she believes she has to face alone and in doing so, she has to leave them behind.
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.
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.
Their shared experiences play a big role. They've been through so much together, like countless battles and adventures. Percy has seen Annabeth in tough situations and he knows how strong she is, but also how vulnerable. So he feels the need to protect her. For instance, they might have had a close call in a previous adventure where Annabeth was nearly killed, and that memory makes Percy extra vigilant.
Their relationship is likely to be complex. They are friends and comrades who have fought side by side many times. So, there's a strong bond of loyalty between them.
A popular one is 'Percy and Annabeth's New Quest'. In this fanfiction, the author takes the duo on a quest that wasn't in the original books. They have to solve ancient riddles and battle new mythical creatures. It stays true to the characters' personalities, making it a great read.