When completing a mission (the third stage), one of two things can happen:

You can get the "end of mission" cinematic (the craft leaving the planet) and possibly the end of chapter text (if this was planet 3 of the chapter), after which you go to the next chapter (which is what SHOULD happen),

Or the game for some reason skips the "end of chapter" text and moves on to a random mission (I've had the game magically skip three planets and warp me to the wrong planet, from planet three to planet six),

Or, and this is where I am stuck, the game just ends. That's right, you win. Even if you're not anywhere near the end of the game. You get "mission complete", and then the ending cinematic and enter high score, then back to main menu. I can't continue playing, as it won't let me pass to the next planet (I just completed Erigone). I keep accidentally winning the game, which sounds ridiculous when I type it.