Godzilla is an obvious choice. The dynamic between Mechagodzilla and Godzilla can create intense and exciting stories. Also, Mothra could be included. Her gentle nature could contrast with Mechagodzilla's more mechanical and often aggressive nature. Another character could be King Ghidorah. The three - headed monster could form an alliance or be in direct conflict with Mechagodzilla in a fanfic.
Striker Eureka. This Jaeger is known for being really powerful. It has some special features that make it stand out in the battles against the Kaiju. And then there's Cherno Alpha. It's a bulky and strong Jaeger that can take a lot of hits and dish out some serious damage as well.
One possible plot could be that Naruto's skills in combat and his ability to form strong bonds would make him a great addition to the Jaegers. He could use his shadow clone jutsu to create multiple distractions during battles against the Kaiju. His chakra could also potentially be used in new ways to power up the Jaegers' weapons or defenses. For example, he might channel his chakra into the Jaeger's sword, making it more powerful for slicing through the tough Kaiju skin.
Another theme is the search for identity. The female Mechagodzilla may be different from the traditional Mechagodzilla, and the fanfiction explores how she figures out who she is in the context of the kaiju world. She could be a hybrid of different technologies or have unique abilities that make her question her origin and purpose.
A Mechagodzilla x Mothra fanfic might explore their different natures. Mechagodzilla, being a man - made weapon of destruction, and Mothra, a symbol of nature and rebirth. The story could be set in a post - apocalyptic world where they have to work together to restore balance. Or perhaps it's a story of how their conflict shakes the very foundation of their world. There could be elements of human interference, like scientists trying to control Mechagodzilla while Mothra tries to protect the natural order.
One idea could be a crossover with the Transformers. Picture Mechagodzilla teaming up with Optimus Prime against a common enemy like an alien invasion force. They could combine their powers, with Mechagodzilla's brute strength and Optimus' leadership and advanced weaponry.
One idea could be a story where Mechagodzilla is reprogrammed by a young genius to protect the city instead of causing destruction. Another could be a time - travel fanfic where Mechagodzilla is sent back in time and has to face off against its earlier versions. Or perhaps a fanfic where Mechagodzilla teams up with other kaiju to fight a common, even greater threat.
Often, a theme of coexistence or conflict is present. Since they are so different, they can either find a way to live side by side in the story world or be in constant conflict. Also, the idea of redemption might be there. If Mechagodzilla is initially a force of evil, it could seek redemption through its interactions with Mothra. And there's the theme of the balance of the world. Their actions can tip the balance towards destruction or restoration.
Naruto's ability to sense danger through his ninja skills could give the Jaegers an edge. In the world of the Jaegers, being able to anticipate the Kaiju's moves is crucial. Naruto could use his chakra sensing to detect the Kaiju's approach from a distance, even if they are hidden. His summoning jutsu could also be interesting. He could summon large toads to help in the fight, either to distract the Kaiju or to assist the Jaeger in some way, like providing a platform to jump from for a more powerful attack.