Perhaps a plot twist could involve the exchange of body parts (a common theme in Fullmetal Alchemist) in RWBY. For instance, a villain in RWBY starts using alchemy to attach different Grimm parts to themselves or others, creating terrifying and powerful hybrids. This not only changes the dynamic of battles in RWBY but also forces the characters from Fullmetal Alchemist to question the ethics of alchemy all over again, as they see it being misused in a new and horrifying way.
One interesting plot twist could be the alchemy of the Fullmetal Alchemist world interacting with the Dust in RWBY. For example, maybe an alchemist discovers a way to transmute Dust into something completely new and unexpected, which throws the balance of power in Remnant (RWBY's world) into chaos. Another could be a character from RWBY somehow getting involved in the Philosopher's Stone plot of Fullmetal Alchemist, leading to a race between different factions in both worlds to either obtain or destroy it.
Well, sometimes there's a plot twist where the Fuhrer is actually being controlled by an ancient alchemical force. This force has its own agenda and is using the Fuhrer's position to further its own goals, like gathering all the Philosopher's Stones in existence. It turns the whole political situation in the Fullmetal Alchemist world upside down and makes for a really engaging read.
One interesting plot twist could be the discovery that the Philosopher's Stone in the Fullmetal Alchemist world has a connection to the chakra system in Naruto. Maybe it could be used to enhance or disrupt chakra flow in a way that no one expected. Another could be a character from Naruto, like Naruto himself, accidentally using alchemy due to some strange cross - world magic. This would completely change the dynamic as he tries to figure out this new power while still having his ninja abilities.
One possible storyline is a cross - over where the ninjas in Naruto are exposed to the equivalent exchange principle of alchemy. They might start using it in their training, like instead of just relying on chakra, they think about what they are giving up to gain a new skill. For instance, a ninja might give up some of his speed to gain more strength. In the case of the Fullmetal Alchemist characters in the Naruto world, they could be involved in the battles between the villages. Alphonse could use his armor body to protect the villagers from attacks. And Scar from Fullmetal Alchemist could have an interesting interaction with the shinobi, as his unique form of alchemy might be seen as a very different type of jutsu.
Edward Elric from Fullmetal Alchemist would probably be very curious about the unique abilities in RWBY, like semblances. He might try to study them from an alchemical perspective. Ruby, on the other hand, would likely be in awe of Edward's alchemy skills and his mechanical arm and leg. She could see him as a kind of mentor in a way.
Well, a great plot twist might be that the characters from Fairy Tail end up in the world of Fullmetal Alchemist and are mistaken for some sort of alchemical creations. They then have to prove that they are not and in the process, they discover that their magic has some strange effects on the alchemy in that world. For example, Gray's ice magic could freeze alchemical reactions in unexpected ways. Another plot twist could be that the Gate in Fullmetal Alchemist has a link to the Fairy Tail's Celestial Spirit World. So when someone tries to open the Gate, they accidentally open a portal to the Celestial Spirit World instead, and all kinds of chaos ensues as spirits and alchemists meet for the first time.
A plot could involve the Avengers trying to understand the concept of alchemy. Maybe Tony Stark becomes really interested in it and tries to incorporate it into his tech. Meanwhile, the Fullmetal Alchemist characters are in awe of the high - tech world of the Avengers. They could end up sharing knowledge and skills to take on a powerful foe that neither could defeat alone. For example, a powerful demon from the Fullmetal Alchemist world that has found a way to use advanced weaponry from the Avengers' world.
One interesting plot twist could be if the alchemical principles in Fullmetal Alchemist were somehow applied to the use of the Rinnegan in Naruto. For example, the Rinnegan's powers being transmuted or enhanced in a way not seen in the original Naruto series.
Well, in some fanfictions, a plot twist is that the harem members start to lose their memories of Naruto. This throws the whole group into chaos as Naruto tries desperately to make them remember. It could also be that a new character enters the harem from an unexpected source, like a crossover within the Naruto universe that has an impact on the Fullmetal Alchemist elements. For example, a powerful shinobi with alchemical knowledge shows up. And sometimes, a plot twist is that the alchemy in the world starts to behave in a strange way that only Naruto can somehow fix, which changes the power balance in the harem and the relationships.
One plot idea could be Scar crossing over into a world where alchemy doesn't exist, and he has to adapt to a completely different form of combat and magic. Another is a crossover with a modern - day world, and Scar has to deal with modern technology and society while still holding onto his beliefs.
A plot could involve a crossover where Pride somehow gets trapped in a human body like the main characters in Fullmetal Alchemist. He has to adapt to human emotions and limitations while also dealing with the alchemists who are initially very suspicious of him. This would be a great opportunity to explore Pride's character in a different light and see how he copes with his new situation.