Perhaps they are banished because they discover a dangerous secret. They could be exiled to keep this secret from spreading. It might be something related to the origin of the Grimm or some hidden power that certain people don't want exposed. And during their banishment, they have to fight to survive in an unfriendly environment.
One possible plot could be that they are banished due to a false accusation. For example, they might be wrongly blamed for a crime they didn't commit within the RWBY universe. Maybe some powerful figure wants to get rid of them for political reasons.
It could be Cinder Fall. She's always been a major villain in RWBY. She might be the one who arranges for Blake and Jaune to be banished as part of her evil plan to gain more power or cause chaos in the world of Remnant.
In some fanfictions, they might team up to prove their worth and get reinstated. They could go on a journey to uncover a conspiracy that led to their expulsion.
It could completely change the dynamic. Their friends would have to deal with their absence, which might lead to some characters going on personal quests to get them back.
In some RWBY Blake pregnant fanfiction, the story could focus on the cultural implications. Since Blake is a Faunus, there could be unique Faunus traditions related to pregnancy. Maybe her pregnancy is seen as a symbol of hope for the Faunus community. The story could also explore how the human characters in RWBY react to this Faunus - related aspect of the pregnancy, and whether it helps bridge the gap between the two races in the RWBY world.
Another plotline might be that Jaune is framed for a crime he didn't commit and decides to disappear to clear his name. He goes into hiding and starts his own investigation, all while his friends in RWBY are trying to figure out what really happened and whether he's actually guilty or not.
A plot where Jaune is the only one in his team who can master a certain martial art that is key to defeating a new type of Grimm. This would put him in a position of great responsibility as he has to train hard and quickly to teach his teammates at least the basics. It creates a lot of tension and character growth as he struggles to become proficient enough to save the day.
Another plot could be that the kidnapping was a case of mistaken identity. The kidnappers thought they were getting someone important but got the wrong person. However, they still hold the character captive, and as the story unfolds, the character has to find a way to convince the kidnappers of their mistake while also trying to escape on their own.
They might be shocked. In many cases, when a character like Jaune is betrayed in fanfiction, the RWBY characters could initially show disbelief as they've come to know him. It would disrupt their view of the group dynamic.
In some scenarios, she might die heroically in a battle against a powerful Grimm. For example, she could sacrifice herself to save her friends from a horde of Nevermores. Another possibility is that she succumbs to an unexpected betrayal within the story, perhaps by a character who was thought to be an ally. Or she could die due to some unforeseen magical or technological accident in the RWBY universe.
Well, Jaune in RWBY fanfiction can vary a lot. Sometimes he's the underdog who overcomes huge challenges, and other times he might have unique powers or a special backstory.