JL5K: doubts

Here's my problem with superhero gaming. I feel like a cook who knows exactly which ingredients to assemble to bake a cake, but doesn't know how to properly mix them to produce cake batter. My main problem lies with plotting. I know I want the climax of the adventure to be a confrontation with Lex Luthor followed by a double twist surprise ending, but how do I get the heroes there? Trying to rough out ideas like this always reminds me why I run dungeon-based adventures: keeping a plot afloat is hard. Hell, coming up with a plot, especially a mystery, is hard as well. What clues do I leave in the scene with the missing planet? If I build set-pieces how can I avoid railroading PCs? Maybe I should just play to my strengths and stick to dungeon adventures or player-empowering indie stuff.