There could be an alien race that has a very different ideology from the people of Remnant. For example, they believe in a survival - of - the - fittest concept at an extreme level. Their leader, who enforces this ideology and leads the invasion, would be the main antagonist. RWBY would have to oppose this leader's cruel ways and protect their own values.
One idea could be that the aliens target the Dust in Remnant as a powerful energy source. The RWBY team has to figure out how to protect it while also learning about the aliens' technology to fight back.
Obviously, Naruto would be one of the main characters. His never - give - up attitude and powerful chakra would be crucial in fighting the aliens. Sasuke would also be important, with his Sharingan and combat skills. Sakura, with her medical ninjutsu, could play a big role in treating the injured ninjas during the invasion. Kakashi could lead the strategic planning, using his vast experience.
A new character created specifically for the fanfiction could be the main antagonist. For example, a powerful being from another dimension who is attracted to the chaos in Remnant caused by the combination of RWBY and Starkiller's presence. This character could have abilities that are a threat to both Starkiller and the RWBY characters, forcing them to work together in ways they haven't before.
Perhaps a half - alien, half - vampire hybrid. This character was shunned by both species and blames Ben for making him feel even more like an outcast. He uses his unique powers to create chaos and tries to turn Ben into a vampire - alien like himself.
Obviously, Harry Potter himself would be one of the main heroes. His experience in fighting dark wizards would give him the courage and skills to face the aliens. Hermione Granger would also be a key hero. Her vast knowledge of magic would be crucial in coming up with strategies against the alien invaders.
Salem would be a great main antagonist in this type of fanfiction. Since she already has a connection to the Grimm, she could use Grim Reaper - like Grimm to further her goals. Maybe she creates a super - powerful Grim Reaper Grimm that can not only kill Huntsmen but also corrupt their souls, making them turn against their own comrades.
It could be a power - hungry general from one of the warring factions. Someone who is willing to sacrifice anything and anyone to achieve victory.
It could be Salem. She has always been interested in the power of the silver eyes, and Ruby having those eyes makes her a prime target. Salem might send her minions to kidnap Ruby, which would lead to her disappearance.
It could be a powerful and corrupted Huntsman. He might have once been a colleague of the Silent Knight but was consumed by greed for power. He now uses his skills to create chaos and try to take over the kingdoms, and the Silent Knight has to stop him.
Maybe there's a hidden character in the Naruto universe who manipulates Naruto into banishing RWBY. In this case, that hidden character would be the main antagonist. They could be someone with a vendetta against RWBY's world or just wants to cause chaos in both universes.