You could write a fanfiction where the Ultra Recon Squad is sent on a secret mission to a different dimension within the Ultra Space. This dimension has its own rules and strange Pokemon. They have to adapt quickly, make alliances with local creatures, and figure out how to complete their mission without getting caught by the powerful guardians of that dimension.
Gladion can also be quite popular. His edgy and mysterious personality, along with his strong Pokemon, can add a lot of depth to fanfiction. He might be portrayed as having a tense relationship with the Ultra Recon Squad at first but then gradually warming up to them.
One idea could be a story where a trainer accidentally bonds with an Ultra Beast during an Ultra Wormhole event. The trainer has to learn to communicate with it and protect it from those who want to use it for evil purposes.
One idea could be exploring the backstories of the lesser - known members in more detail. For example, showing how they got their powers or what led them to their criminal lives.
I'm not sure about the exact plot as I haven't read it yet. But generally, in a graphic novel, it could be about a group of characters with special abilities (since it's 'ultra squad') going on adventures, facing challenges, and probably saving the world or something similar.
One idea could be Naruto discovers a hidden ancient jutsu that unlocks his ultra instinct - like powers. He then uses these powers to quickly defeat enemies in the Fourth Great Ninja War, surprising everyone including Sasuke. Another could be Naruto training in a secret dimension where he gradually attains ultra instinct and has to face off against a new, powerful and unknown enemy that threatens the entire ninja world.
One idea could be an OC who is a former criminal turned informant for the Ghosts. They have unique skills from their past life that help the team in unexpected ways. For example, they know all the secret passages in the drug cartel's strongholds because they used to work with some of the lower - level members.
Maybe the RWBY characters end up in the world of Ghost Recon. They would be in a completely different environment, with no Grimm but new threats like human enemies. The RWBY characters would have to adapt their fighting styles. Ruby, with her speed, could be used for quick reconnaissance missions, while Weiss could use her Glyphs in creative ways to assist the Ghost Recon team in combat situations.
One idea could be a crossover with another military - themed game like Call of Duty. The Ghosts could team up with the COD characters to take on a global terrorist threat that neither could handle alone. They would have to combine their unique skills and weaponry.
One idea could be an OC who has a unique dino - like ability that the regular Dino Squad doesn't have. For example, the ability to communicate with prehistoric plants. This could add a new dynamic to their adventures as they might discover hidden secrets or threats related to these plants.
One idea could be that Naruto somehow gets transported to the world of Dino Squad. He teams up with the Dino Squad members to fight a common enemy that has the power to disrupt both their worlds. For example, a powerful ninja from Naruto's world who has teamed up with an evil scientist from the Dino Squad world to create chaos.