As for the plot, perhaps we could be on the run because the both of us have found files about the magical genes that could be exploited? It'd also work well as one character chasing the other; if we took upon something more intincrate, it could be changing the way society views magic, or something around that idea. Something big.

And characters... well, that's a hard question right there. If I had a magic user, I'd probably be some spoiled, sheltered rich kid who looks down on non-magic users; an idiot who's easily manipulated. I guess it'd progressively advance from there, for better or worse. I could also be some activist against the people who abuse magic (a blind idealist), or a mage who collaborated with the researchers of the gene in order to improve humanity. There's a ton of possiblities, really. As a non-magic user? There's even more. It could be some disgruntled individual with a hatred for all things related to magic, it could be someone on a quest to acquire magic powers for himself (as for the reason, there are plenty of possiblities) or a researcher that accidentally found the materials of the files and got caught up in an ordeal.

Tell me if you like any of these ideas, I am just throwing 'em out there.