Thank you for your feedback, it's very valuable.
Like you've guessed, this isn't how the game is supposed to be play, basically, the longer you wait before pressing space, the more powerful your action is, and if you press space while the clock is on the green, you get a bonus to your damage or heal. The clock is just a tool to help the player find a rhythm, so the boss breaks it because he's evil!
Your comment really highlight that we need to make it more obvious how the game is intended be played, but we didn't have time to make a tutorial level despite wanting to; that's why the "how to play" section is so long and not great.
Thank you for your kind word, we're working on upgrading the game, for example, clicking now also make the countdown work.