One idea could be that the Autobots and Maximals team up against a new common enemy that has the ability to corrupt both mechanical and organic forms. They would have to combine their different skills and technologies to overcome this threat.
Perhaps a story where a human somehow gets transported into the Beast Wars universe and has to help the Maximals and Autobots communicate better. This human could introduce new strategies and ways of thinking that the Transformers hadn't considered before.
One idea could be a crossover with the Transformers Prime series. Imagine the Beast Wars characters interacting with the more modern Transformers designs and storylines from Prime. It could lead to some really cool battles and character development as they learn from each other's different ways of dealing with the Autobot - Decepticon conflict.
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 a crossover where the characters from Transformers Prime end up in the Beast Wars universe. They could form alliances with the Beast Wars characters to fight a common enemy like the Predacons. Another idea is to explore the origin stories of some of the Beast Wars characters within the context of the Transformers Prime lore. Maybe there's a hidden connection between a Prime character and a Beast Wars character that could be uncovered.
Perhaps Vergil is from a parallel dimension where the Devil May Cry world and the Transformers Beast Wars world are already intertwined. He comes to the Beast Wars universe to seek a powerful artifact that could help him in his own dimension's battles. Along the way, he forms unexpected alliances with both Autobots and Maximals, and his presence changes the course of the Beast Wars as the different factions either see him as a threat or an opportunity.
One idea could be exploring a hidden planet during the Dark Voyage. The Maximals and Predacons could discover a new energy source there that changes the power dynamics. Maybe there are ancient Transformers on this planet with unique abilities.
One idea could be that Lucifer, with his charm and manipulative skills, gets involved in the power struggles among the Autobots and Decepticons. He might try to use their war for his own amusement or to gain some sort of power. For example, he could offer a deal to Megatron to help him defeat the Autobots in exchange for something valuable in the underworld.
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.
Well, a cool concept for a Ben 10 Transformers crossover fanfiction could be that the Transformers' AllSpark has a strange effect on the Omnitrix. This makes Ben able to transform into new alien - Transformer hybrids. For instance, Four Arms could become a huge hulking form with robotic arms that can transform into different weapons. Also, the Decepticons might try to steal the Omnitrix to use its power to create more powerful soldiers. Meanwhile, the Autobots would team up with Ben to stop them. Maybe there could be a situation where Ben has to use his alien forms' unique abilities in combination with the Autobots' skills to defeat a powerful Decepticon threat.
One idea could be that Sonic and his friends accidentally stumble into the world of the Transformers. Sonic's speed could be a valuable asset in a battle against the Decepticons. For example, he could quickly deliver important messages or parts between Autobots during a fight. Another idea is that the Chaos Emeralds somehow have an impact on the AllSpark, creating new powers or challenges for both the Sonic characters and the Transformers.
Another interesting concept is to have a character crossover. For example, Bumblebee from the Animated series could somehow end up in the world of the live - action Transformers movies. His small and agile form might be a big contrast to the more bulky Transformers in the movies. He could form an unexpected friendship with a human character, like Sam Witwicky, and together they could help the Autobots in the movieverse with a mission that requires his speed and intelligence.