A great Percy Gaea fanfiction could explore Percy's journey of discovery about Gaea's past. He might find out that there were certain events in Gaea's history that led her to become the way she is. By understanding her better, Percy could try to find a more peaceful solution to their conflict rather than just fighting.
There might be a fanfiction where Percy forms an unlikely alliance with Gaea. Maybe Gaea is not entirely evil in this story, and they have to work together to face a greater threat that endangers both their existences. This would be a really interesting take on their relationship.
In some fanfictions, Gaea's love for Percy could be a curse placed on her by some other deity. Percy initially is repulsed but as the story progresses, he realizes that there's more to Gaea than just the evil being he knew. The fanfic could then delve into how they both try to break the curse and in the process, understand each other better. It could also involve other characters from the Percy Jackson series reacting to this strange relationship.
The fanfiction 'Gaea's Unseen Realm' is very creative. It takes the idea of Gaea's domain and expands it into a whole new world. The author creates unique creatures and landscapes within Gaea's realm that are both beautiful and terrifying.
One plot idea could be Gaea's redemption. In the original series, she was a major villain, but in a fanfic, she could be given a chance at redemption. Maybe Percy and his friends discover that Gaea was being controlled by a more powerful and malevolent force all along, and they have to work with her to defeat this greater evil.
One idea could be Percy having strange, prophetic dreams about Gaea that lead him on a quest to understand her true nature before she fully awakens. Maybe he discovers an ancient bond between them that was long forgotten. Another could be Gaea trying to tempt Percy to join her side by offering him power and the ability to reshape the world in a way he might think is better. For example, she could show him a vision of a perfect world without the constant threat of monsters, but with a hidden, dark price.
One idea could be Percy having to face challenges in a world where Gaea has more direct control over the elements. For example, the earth itself could be constantly shifting and changing, creating new terrains and obstacles for him to overcome. Another could be Percy forming an unlikely alliance with some of Gaea's other children who are also having second thoughts about their mother's destructive plans.
One idea could be that Percy has a dream where Gaea is trying to corrupt the power of a magical lemon tree. The lemon tree has the ability to heal demigods, but Gaea wants to use it to create chaos. Percy, with his friends, has to protect the tree. Maybe the lemons from the tree can also be used as weapons against Gaea's minions, like when thrown, they release a burst of purifying energy.
Perhaps the Daughter of Gaea is sent on a mission by Gaea to infiltrate Camp Half - Blood. But instead of causing harm, she falls in love with the sense of community there. She starts to secretly help the campers prepare for Gaea's attacks. She could use her connection to the earth, which is different from the demigods' but still useful, like sensing when Gaea is about to send her minions.
I'm not sure of specific titles, but a good fanfiction in this regard might be one where Gaea's love for Percy is a result of seeing a future where they could rule together. Percy, of course, has to decide if he wants to be part of such a future or fight against it.
A really interesting plot could involve Percy being in a situation where he has to use the powers he inherited from Gaea to save the world from a new and greater threat. However, the other demigods don't trust him at first. So he has to not only fight the external threat but also earn the trust of his comrades. He might discover ancient secrets about Gaea that could either doom or save the world, and he has to make a difficult choice based on that knowledge.
One idea could be Percy having to choose between the powers of Kronos and Gaea. Another could be Percy teaming up with some unexpected allies from the realms of Kronos and Gaea to fight a new common enemy. Maybe Percy discovers a hidden prophecy that involves his lineage as the son of Kronos and Gaea and has to fulfill it to save the world.