Identity reveal fics are incredibly common, though most of these at least end on a happy note.  In Danny Phantom canon, he was able to choose when to reveal his half-ghost status to his ghost-hunting parents when they'd changed enough to accept it.  Phantom of Truth shows what could happen if Danny's mom ever got the chance to ignorantly experiment on his ghost half. The story starts off with mostly harmless experiments but they soon escalate to things that no human should experience. Danny's emotional scarring at the torture goes deep and it, along with his mother's trauma at realizing what she did to her own son, is explored in the sequel Shadow of a Doubt.

Depths is the first of a four-part series of one-shots that takes a plot twist of Young Justice, that one of the team goes deep-undercover, and makes it so that Nightwing has to go undercover instead.  The team's sense of loss after Nightwing's apparent death stings even more and Nightwing is willing to do worse things than the canonical mole did to keep his cover intact, no matter how much he will hate himself for it.  This story highlights a theme that was apparent in the original cartoon, of how morally gray it is to put your own friends in danger for the greater good, and just intensifies it until it becomes nigh impossible to recover from.

Sisyphus is a dark take on a common feature of fanfics where a character goes back in time and has the chance to change things.  In this story, though, Harry is sent back repeatedly against his will à la Groundhog Day.  With each cycle, Harry tries to make changes but doing so only gets him killed to start things over again.  After over a hundred attempts, he makes what ought to be a perfect run to free him.  It doesn't work.