Perhaps Ruby is brainwashed into believing she has a different past or purpose. This could lead to her making choices that are out of character, and the story could explore how her true self starts to break through the false memories and programming. It might also involve her friends using their unique abilities and relationships with her to help her regain her true self.
One idea could be that Ruby is brainwashed by an enemy to turn against her team. Then her friends have to find a way to break the brainwashing and bring her back. This could involve a lot of emotional scenes and intense battles.
Another plot idea could be that the brainwashing is part of a larger conspiracy within the RWBY universe. Ruby's brainwashing could be just one piece of a much more complex plan by a powerful villain. As the story unfolds, not only do her friends have to save Ruby, but they also have to uncover and stop the entire conspiracy, which could involve many other characters and different locations within the RWBY world.
One idea could be Ruby adjusting to her new cyborg body and the enhanced abilities it gives her, like super - strength or advanced weaponry integration. Another could be her facing discrimination from some in the RWBY world who fear or mistrust cyborgs.
One plot idea could be Ruby discovering she has werewolf abilities during a mission. She has to learn to control it while still fighting Grimm. Another could be that in a werewolf form, Ruby has enhanced senses that help her track down a powerful and elusive enemy. Or perhaps she forms a pack with some of her friends who also get werewolf-like powers and they have to protect Vale from a new werewolf - Grimm hybrid threat.
One idea could be Ruby discovering she has some cheetah - like abilities. Maybe she's faster than ever and has to learn how to control this new power. It could add an interesting dynamic to her combat style and how she interacts with her team.
One idea could be that Ruby and Coco team up for a special mission in a dangerous, uncharted part of Remnant. They face new Grimm and have to rely on each other's unique skills to survive. Coco's fashion - sense - related weaponry could combine with Ruby's speed and scythe skills in interesting combat sequences.
A really interesting plot would be if Ruby's Reaper form was somehow connected to an ancient prophecy in the RWBY world. Maybe it was foretold that a Reaper - like figure would either save or doom Remnant. This would put Ruby in a very difficult position, with different factions having different views on her and her new form. Also, a plot where Ruby has to team up with some unlikely allies while in her Reaper form to take on a common threat could be cool. These allies could be former villains who see the greater danger that requires Ruby's power.
One idea could be Ruby having to relearn her combat skills while being deaged. It would add an element of struggle and growth as she tries to regain her former abilities. Maybe she forms new friendships with characters she already knew in a different way because of her new, younger perspective.
One plot idea could be Ruby discovers she has werewolf abilities during a mission in a forest. She has to learn to control it while still fighting the Grimm. Another could be that there's a curse in Beacon Academy that turns Ruby into a werewolf, and her friends have to find a way to break the curse without hurting her.
A third plot idea could be Ruby having to face an ancient vampire threat that is related to her new condition. Maybe she discovers that she was turned into a vampire as part of a bigger plan by an evil vampire lord, and she has to stop this villain while also coming to terms with her own vampirism. This could involve her learning about vampire lore and using it to her advantage.
One idea could be Ruby facing a new type of Grimm that has unique abilities, like the ability to manipulate time in a small area. This would put Ruby in a tough situation where she has to figure out how to combat it while being affected by the time distortion. Another plot could involve Ruby getting lost in a Grimm - infested area and having to rely on her wits and the little resources she has to survive and find her way back to her team.
Perhaps the story could explore how Ruby's pregnancy affects her relationships with her team members. Some might be overly protective, while others could struggle to accept the change in her situation. It could also be interesting to see how her pregnancy impacts her relationship with her weapon and combat abilities.