First, you need to be familiar with both the RWBY and Magic: The Gathering universes. Know their characters, settings, and rules. For example, in RWBY, you have the different academies and the concept of Aura and Semblance. In MTG, there are the various planes and the unique magic systems. Then, come up with an interesting concept for your fanfic. It could be a crossover event, like a Planeswalker coming to RWBY or vice versa.
Well, if you're aiming to write an 'mtg rwby fanfic', start with the basics. Decide whether you want a more action - oriented story, a comedic one, or something more character - driven. Then, do your homework on the two franchises. In RWBY, there are so many unique characters with distinct personalities and abilities. In MTG, there are different races and magic types. You can start by writing a short scene, like a meeting between a RWBY character and an MTG creature. Build on that, adding more details about the setting, the conflict, and how the characters will overcome it. You can also look at other fanfics for inspiration, but make sure to put your own spin on it.