A possible plot for a fanfiction about Whitley and Ruby in RWBY could be that they are both chosen for a special task by Ozpin (or his successor). They are the least likely pair to be chosen together, but as they work on the task, they find out that they complement each other well. Whitley's knowledge of Atlas society and technology, combined with Ruby's combat skills and leadership, make them a formidable team. Along the way, they might face challenges from within the group that doesn't believe in their partnership, but they prove everyone wrong by achieving their goals successfully.
One plot idea could be Ruby and Winter teaming up for a special mission. Maybe they have to infiltrate an enemy stronghold. Ruby's speed and Crescent Rose could be combined with Winter's ice powers and combat skills for some epic fight scenes.
One plot idea could be Qrow training Ruby in some special combat techniques that are unique to his own fighting style. This would allow Ruby to gain new skills and also strengthen their bond as family members.
One idea could be Ruby trying to understand Salem's motives beyond just destruction. Maybe she discovers that Salem has a tragic past that led her to this path and Ruby attempts to find a way to redeem her. Another plot could involve Salem targeting Ruby specifically because of her silver - eyed powers and Ruby having to outwit Salem in a series of battles.
Another plot could involve Ruby and Arslan getting into a friendly competition. They could be competing in a tournament within the RWBY universe. This would show their different fighting styles and how they learn from each other during the competition. They might start off as rivals but end up as good friends.
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.
For Whitley, he could start off as a cold and aloof character, but through his interactions with Ruby, he could become more empathetic and caring. Maybe he realizes that there's more to life than just status and wealth. For Ruby, she could learn to be more patient with people like Whitley who come from a different background. She might also develop a better understanding of the complex social structures in Atlas.