You can get secret modes by beating the game. Beat the game in any difficulty to aquire Special Continue, Trial missions, FMV sequences, 36 musics from the game, and be able to change the color of your aircraft.

Beat each mission in normal difficulty with an S-rank to unlock the secondary color for each fighter. By shooting down the aces you get the 3rd. You don't need to pass the trial missions for the 2nd colors.

Beat the game on normal and get an S rank for every mission to unlock all the aircraft, including the X-02 Multirole fighter.