One possible plot could be that the male Indoraptor and the Indominus Rex form an alliance against the humans who are trying to control them. They might start off as enemies but gradually realize they have more in common than they thought.
Another option is to check out some Jurassic World or dinosaur - themed fanfiction forums. The fans there might be able to recommend some great stories in this particular pairing. They could also give you some insights on the most interesting plotlines in such fanfics.
One idea could be a story where Godzilla and Indominus Rex are forced to team up against a common, even more powerful enemy. Maybe an alien invasion that threatens to destroy their world. They start off as enemies but gradually learn to work together.
Naruto might try to befriend the Indominus Rex. He's always been one to see the good in others, even enemies. So he'd probably approach it with an open heart. Sasuke, on the other hand, would be more cautious and likely see it as a threat to be eliminated if necessary.
A possible plot could be that Indominus Rex somehow gets teleported into Godzilla's world. Confused and angry, it starts attacking everything in sight. Godzilla, seeing this new threat, decides to take it on. Their battle could cause massive destruction, but in the end, they might reach a truce when they both realize there are bigger threats out there.
A frequent theme is the relationship between the two. It could be a friendship that defies the odds, as a human and a dangerous dinosaur becoming friends. Also, survival is a common theme. They might have to survive in a world full of other threats together. There can also be a theme of mystery, where the Indominus Rex has some secrets that the reader tries to figure out.
One reason Indominus Rex human fanfiction is appealing is the contrast between the two. The Indominus Rex is a huge, fierce dinosaur, and humans are relatively small and frail. The stories can play on this contrast, creating high - stakes situations.
A fanfiction might explore the Indominus Rex transformation in a more magical way. Suppose there is an ancient artifact in the park that emits a strange energy. When the Indominus Rex comes into contact with this energy, it starts to transform. Its body becomes larger and more muscular, and it gains the ability to breathe fire. This new power would turn it into an unstoppable force in the park, and the other dinosaurs would have to either flee or team up to face this new threat.
There might be a fanfiction where the reader is a scientist in the Jurassic World and has to work closely with the Indominus Rex. As they interact more and more, they start to understand each other on a deeper level, and there are a lot of tense and exciting moments as they deal with the power of the Indominus Rex.
Perhaps a post - apocalyptic world where an Indominus Rex and a group of humans form an unlikely alliance. The Indominus Rex, being a powerful predator, helps the humans fend off other dangerous dinosaurs in exchange for food and shelter. The story could explore the trust and fear dynamics between the two species.