When he is sent to investigate a billionaire with a deadly artifact, in in a world where the line between natural and supernatural is growing thin, a preteen magical spy must return the artifact in return for medicine for his dying sister; but when his cover blown, it must learn to work with his arrogant rival in order to fight his way to the mission’s end before the artifact destroys the city.

An intriguing concept! As for the Logline itself, I do think that some of the information should be condensed and perhaps rearranged. For example, start with the main character and then establish the event which leads to his preceding action. Something like, 'A pre teen spy with an aptitude for magic has his cover blown by a nefarious billionaire and must escape his wrath with the help of his long time rival.' or something to that effect. I personally think a logline works best when it establishes the stakes of the characters or their conflict on a personal level, instead of the bigger picture, because if an audience can be hooked by the personal stakes, that the bigger picture stakes will become a natural progression as the story goes on. Please keep developing it, this sounds fun!