when you say "...no clue how to apply..." are you having problems with the type of questions the door should ask? it could ask math questions [10+50= what] and a pop up screen comes with 3-4 answers and the player has to select the correct one.
or are you having problems implementing it? a portion of the game could be a top down shooter where to destroy enemies to collect a certain amount of XP and when you have enough XP points, then your ship warps to the door/gate way where you have to solve the riddle to get past?
not sure what you're having concerns with, but hope this help in a little way.