I'm not sure specifically as there could be many novels with such a title. It might be about three characters who are in some sort of secret alliance or mission. Maybe they are trying to solve a mystery or fight against some sort of evil.
There's no way to know exactly without reading the novel. They could be three adventurers, like a brave warrior, a clever mage, and a sneaky thief. They might each bring unique skills to the group, which are crucial for their adventures in the story.
For Rayquaza, you can develop it as a wise and powerful protector. Show it observing the world from high above and only interfering when there's a major threat to the balance. Groudon could be developed as a proud and somewhat stubborn character, with a deep connection to the land. Kyogre can be a more mysterious and fluid character, its actions often driven by the ebb and flow of the oceans. For example, you could write about Rayquaza teaching a young Pokemon about the importance of balance in nature.
The Penguin could be the most interesting. He's got his devious mind and his connections in the criminal underworld. His umbrellas and other gadgets add a unique touch to his criminal activities. He could be the mastermind behind the Terrible Trio's plans, using his wits to outsmart Batman.
The members of the Pokemon Creation Trio can vary depending on the fanfiction. However, common ones might include Dialga, representing time; Palkia, representing space; and Giratina, representing anti - matter or the distortion world.
The founders might be quite surprised by the Golden Trio. They could be impressed with their skills and knowledge. For instance, Hermione's vast magical knowledge would surely catch their attention.
The characters in the 'dark trio' in the fanfiction are likely to be those who have a propensity for the dark arts or have some sort of malicious intent. It could be that the author takes minor characters from the original series and gives them more prominent roles within this dark context. For example, Crabbe and Goyle could be developed further into more menacing characters, or perhaps some of the Death Eaters that were not as well - explored in the original books could be part of this trio.
They'd probably start off being really cautious around each other. The Golden Trio would be cautious because the Winchesters seem so different and rough. The Winchesters would be cautious as they're not used to this kind of magic. But then Hermione might start asking questions about the Winchesters' hunting methods and Dean would start joking about the Trio's school - like magic.
Well, Sans is a key character. He brings his cynical and sometimes devious nature to the group. Papyrus is there too, adding his own brand of naivete and energy, which often contrasts with Sans. Grillby, the fire elemental, is also part of the trio. His calm and collected demeanor provides an interesting balance to the more volatile personalities of Sans and Papyrus. Together, they create a dynamic that drives the story in many bad time trio fanfictions.