Maybe a story where a character from RWBY discovers a lost Transformer in the wilderness. This Transformer could be damaged and in need of repair. The RWBY character, with their unique skills, tries to help the Transformer while also learning about its origin and the greater universe it comes from. This could lead to a deep friendship and an exchange of knowledge between the two different worlds.
One idea could be a crossover where the Autobots from Transformers Prime end up in the world of RWBY. They could team up with the RWBY characters to fight a common enemy, like a new type of Grimm that has some technological abilities similar to the Decepticons. The Autobots' advanced weaponry and technology would be a great addition to the RWBY universe's combat.
One idea could be exploring Predaking's origin in more depth. Maybe he has memories from before his creation that he slowly uncovers. Another could be a story where Predaking tries to form an alliance with the Autobots against a common enemy, like a new and powerful Decepticon threat.
Maybe the Transformers end up in Remnant due to a space - time rift. The Grimm might be attracted to the Energon that the Transformers carry. The RWBY teams would have to team up with the Transformers to fight off both the Grimm and the Decepticons if they also show up. Yang could learn some combat moves from the Autobots, which would add a new dimension to her brawler style.
One idea could be a crossover with the Autobots from Transformers Prime and the Titans from Attack on Titan. Imagine the Autobots having to fight the Titans in a post - apocalyptic world. Another idea is a crossover with the Power Rangers. The Rangers and the Autobots could team up to fight a common enemy that threatens both their worlds. A third idea might be a crossover with the Teenage Mutant Ninja Turtles. The Turtles could use their ninja skills along with the Autobots' firepower to take on a new threat in New York City.
One plot idea could be that Female Optimus Prime has to lead a team of misfit Autobots to save a planet from a new, powerful Decepticon threat. She has to use her unique leadership skills and strength to unite the team.
You could write a story about a young Autobot or Decepticon who gets stranded in the Beast Wars era and has to learn how to survive among the Maximal and Predacon factions. They might have to adapt to the different rules and cultures while also trying to find a way back to their own time.
One idea could be exploring Starscream's origin as a 'baby' in the context of the Transformers Prime universe. Maybe he was created with a special purpose that was later forgotten or corrupted.
There could be a fanfiction where Bumblebee loses his memory. Arcee takes it upon herself to help him regain it. She takes him to all the places they've been together, shares their memories, and tries to jog his memory. As she does this, she also realizes how much Bumblebee means to her and how important their relationship is. This is a story about friendship, loyalty, and the power of memories.
One idea could be an OC who is a medic that gets captured by Megatron. Megatron initially sees the OC as a tool to use against the Autobots but gradually develops an odd respect for the OC's skills and tenacity. Another plot could involve an OC who has a special power that Megatron wants to harness for his own evil plans. As he tries to manipulate the OC, the OC starts to see through his lies and tries to turn the tables on him. A third plot might be an OC from a different dimension who accidentally lands in the Transformers Prime universe and catches Megatron's attention. He's intrigued by this strange new being and tries to either recruit or destroy the OC.
One idea could be that Optimus Prime travels back in time to prevent the creation of a powerful Decepticon weapon. This would change the whole course of the war. Another could be a human character traveling to the future of the Transformers' world to see how the conflict ends and bring back knowledge to change the present situation. And perhaps a Decepticon time - travels to the past to rewrite history and make themselves the rulers from the very beginning.
Perhaps a fanfiction where Soundwave gets damaged in a fight and Megatron has to make a difficult decision about whether to risk everything to save him. It could explore their loyalty to each other. Or a plot where they are betrayed by one of their own and they have to work together to expose the traitor.