Don't fear the water and check out every corner. The GB rom is complete. I just finished the game.
Thanks! I started a new game, and at around 8 energy the jetpack started working! That never happened on my first play-through. That's why I was stuck. Maybe a bug? I was able to finish the game this time, although strangely I ended up with 29 energy instead of 25. I collected the same 4 twice each because they reappeared somehow. There's also a place where I was able to spam unlimited energy during the first play. Odd behavior around energy might be a bug? Despite that, it's a great Zelda-esque game! :)