An Alternate Reality Game (ARG) is an interactive storygame hybrid whose core mechanics include collaborative problem solving and storytelling. ARGs are also participatory experiences, because game designers dynamically adjust content in response to players' actions as game play progresses. What if the participatory process was extended during the design phase of an ARG as well? Few, if any, studies have explored how to include player populations in the ARG design process - especially ARGs that target youth. In this paper, we share the process we followed to design a large-scale ARG to promote scientific inquiry for teenagers (13-17 years old) by partnering with them. Our findings suggest that co-designing with youth resulted in novel design features in the final game, and gave us insight into adolescent attitudes toward various scientific concepts. We also share co-design techniques that were not as effective and offer suggestions for future approaches.