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The skybox is really just a flat gradient that is a child of the camera, placed at a distance so that it will cover the whole viewport. The clouds are made using a particle system of meshes with a semitransparent material. As for the "flat effect"? I'm not sure exactly what you're referring to, but I set the edges for many things as "flat" in Blender (3D modeling tool) as opposed to "smooth" to give it that faceted lowpoly look.