One interesting storyline could be Hermione leading a secret study group within the Order of the Phoenix to research new spells against Voldemort. This could show her leadership skills and intelligence in a different light compared to the original books.
Another possibility is that Hermione, as a sorceress, has to face challenges within the Hogwarts community. For example, some students might be jealous of her powers and try to undermine her. But she overcomes this with her intelligence and the strength of her magic. In this type of fanfiction, we could see her form new alliances and learn new ways to use her magic to defend herself and those she cares about.
One interesting storyline could be Snape taking Hermione on as a special apprentice of sorts. He sees her potential in potions and dark arts defense far beyond her years and decides to privately tutor her. This could lead to a series of adventures where they explore ancient spells and potion-making techniques together.
In many Hermione is a Phoenix Princess fanfictions, there are storylines centered around her relationship with Harry and Ron. Maybe her new powers cause some strain in their friendship at first, as they struggle to understand how she has changed. But then they come together to face a common enemy. Also, some storylines might involve Hermione using her phoenix powers to resurrect a fallen character, adding an element of hope and redemption to the story.
Signs could include the Order withholding crucial information from Hermione that endangers her. Suppose they know of a Death Eater plot specifically targeting Hermione but don't warn her. Or if they start to treat her with suspicion and start monitoring her every move like she's an enemy, when she has been nothing but loyal to their cause. But again, these are very much against the normal characterization of the Order in fanfiction, as they are usually a united front against the Dark side and Hermione is an important part of that fight.
Some fanfictions might explore what would happen if the Order of the Phoenix had more insider information about Voldemort's plans. For example, they could have a spy within Voldemort's inner circle that changes the whole dynamic of the fight. This would lead to different battles and strategies. Also, there could be a fanfiction that delves into the emotional state of the students at Hogwarts during this time, like how Ginny copes with the return of Voldemort and her feelings for Harry in a more detailed way.
Well, there could be a story where Hermione discovers a hidden diary of Lily Potter. As she reads it, she starts to adopt some of Lily's characteristics and wisdom. This could lead to her becoming a more empathetic and powerful witch, and also might help her in her relationships with Ron and Harry. In a different plot, Hermione could be magically transformed to look like Lily for a special mission, and during that time, she experiences the world from Lily's perspective, which changes her in many ways.
Another could be a love triangle between Hermione, Edward, and Jacob. Hermione's intelligence and strong will might make both of them attracted to her in different ways. She could be torn between Edward's brooding charm and Jacob's more down - to - earth nature.
One interesting plot is when Draco is forced to work undercover for the Order of the Phoenix. It turns his world upside down as he has to deceive his Death Eater family. Another plot could be Draco falling in love with a member of the Order, which creates a huge internal conflict for him.
One interesting plot twist could be that Hermione discovers a hidden prophecy within the Order of Phoenix that directly relates to her and her friends' destinies. This could lead to a whole new set of adventures and challenges as they try to figure out what it means and how to prevent or fulfill it.
One common theme is the deepening of their relationship. Fanfictions often explore how they grow closer during this difficult time at Hogwarts. Another theme is their contribution to Dumbledore's Army. They are shown as key players in the fight against Umbridge's tyranny.