Family drama. The Weasley family has its fair share of chaos. His relationship with his family members, especially after some of the disagreements he had, could be a source of emotional stress that manifests as migraines. For example, his estrangement from his family during a certain period in the books could have taken a toll on his mental well - being.
One reason could be his regret over his past actions. For example, when he distanced himself from his family to pursue his career at the Ministry. He might realize later how wrong he was and cry out of remorse.
Perhaps it's a symbol of his new - found independence. After leaving his family and then potentially coming back, he might be exploring new things. Smoking could be part of that exploration, something that he wouldn't have considered before. Also, it could be used to add an air of mystery or edginess to his character. Fanfiction writers often use such elements to make a familiar character seem more complex and interesting.
One place to look could be Fanfiction.net. There are often many Harry Potter - related fanfictions there, and you might find some that focus on Percy Weasley getting migraines. Just search for relevant keywords in the search bar.
One reason could be to add more conflict within the Weasley family. Percy was already somewhat of an outcast in the family due to his loyalty to the Ministry. Turning him into a Death Eater would intensify that divide.
Well, it could be related to Percy's past actions. If he has a history of being unreliable in the eyes of the character rejecting him, that would be a valid reason. For instance, if he has broken promises in the past. Or perhaps there are external factors at play. Maybe the family of the person rejecting Percy doesn't approve of him, so they influence the decision. Another aspect could be that Percy is too different in terms of values. If he values adventure and risk - taking above all else and the other character values stability and safety, it can lead to a rejection.
Perhaps Draco has been bullying some of Percy's friends or younger students that Percy feels responsible for. In fanfiction, the relationships can be tweaked a bit. Percy might be more hot - headed in some versions and not put up with Draco's pure - blood supremacist attitude towards those he deems as 'lesser' students. So he sends the Howler as a strong warning.
Well, Percy is often neglected in fanfiction because he doesn't have the same kind of popularity as the main characters. In the books, he's not part of the core group that goes on the big adventures. He's more into the rules and regulations of the wizarding world. Fanfic writers usually prefer to write about characters who are more involved in the action - like Harry facing Voldemort. Percy's role in the official story is more of a background one in terms of the main plot, so it's easier for him to be overlooked in fan - created stories.
Annabeth is a very determined and strong - willed character. In her mind, Percy is part of her 'territory' because she has fought beside him and for him. She may feel that she has a claim on him, and this sense of ownership makes her territorial.
In some fanfictions, Ginny might be written to betray Harry because of a prophecy. The prophecy could mislead her into thinking that Harry was going to bring doom, and so she decides to act against him to prevent that. It's a different way of looking at their relationship compared to the original story, where their bond was based on love and trust.
She could be banished due to her unorthodox powers. In many fictional settings, if a character has powers that are different or not understood by the majority, they are often feared. If female Percy has some unique abilities that are considered dangerous or abnormal, the authorities or those in charge might decide to banish her to keep the peace or protect their own interests.