- Gotham Adventures #13, in which the Threatening Trio wind up disbanding with Mr. Nice leaving the country to fulfill a prophecy by helping a young boy. It ends with him leaving into a bright light. It becomes incredibly more sad when you see the real life context: Mr. Nice had been created to resemble comic writer Archie Goodwin, who had died earlier that year; the issue was made in dedication to him.
- The ending of Batman & Robin Adventures #7.
- Gotham Adventures #37. It starts out with a lot of Silver Age Batman antics, only to reveal that Batman had actually been captured by the Mad Hatter and put in a fantasy dream world the whole time. When Batman gets free and asks Hatter why he'd done it, the reply is heartbreaking.
Mad Hatter: Well, because you always seemed so unhappy. Every time we met you always won, and yet it didn't seem to bring you any joy. In fact, I thought you were the saddest person I'd ever met. So I just tried to help you.
- Made worse by the fact that the reason Bruce realized that the world was fake was because he felt happy. That was the thing that made him distrustful of the dream. He hasn't been happy since his parents died.
- The tribute to DC artist Mike Parobeck in Batman & Robin Adventures Annual #1.
- "No, Ms. Gleeson. The person you described....was never here...."
- Explanation: The woman's boyfriend was Clayface, desperately seeking some normalcy in a relationship with her while plundering Gotham. Batman catches him; Clayface could escape if he took his human form, but when he sees her nearby, he refuses to ruin her image of him and begs Batman not to fink him out.
- Talia to Batman, right after her Face–Heel Turn: "If I had told you, we wouldn't have had Paris...."
- There's a Christmas special that features Mr. Freeze icing over Gotham with a manufactured blizzard. Dr. Leland explains that as it got closer to Christmas with the forecast suggesting no snow until after New Years, Victor became more and more agitated, until he finally broke out. When Batman finally disables him, he gives him one chance to turn himself in peacefully, tiredly demanding to know why he would cause trouble on Christmas Eve, of all days. In response, Victor points at Nora's tombstone.
- Mad Love. It holds even more weight than the cartoon adaptation, and you can't help but pity Harley.
- The Riddler, after escaping Arkham and deciding to give Batman clues to other people's crimes, somehow subconsciously forms a three-part riddle to his own location. His realization is heartbreaking.
Riddler: You don't understand. I really didn't want to leave you any clues. I really planned never to go back to Arkham Asylum. But I left you a clue anyway. So I...I have to go back there. Because I might need help. I...I might actually be crazy...
- Victor's letter to Nora at the end of Gotham Adventures #51 after a drawn out episode of Yank the Dog's Chain involving Clayface impersonating her. Deciding that she couldn't possibly love him anymore, he says goodbye and that she's made the right choice by moving on, escaping Gotham for a life in the Arctic. Cue Nora arriving at Arkham Asylum asking for Victor Fries. To make it worse, the only reason why she hadn't gone to see him sooner is because her new husband was hiding the other letters he sent.
- The three part arc in #34-36 that capped off the original series features Bruce getting most of his memories stolen, regressing him mentally to that of a 7-year-old, long before the night his parents were taken from him. Seeing him act happy and cheerful hurts when you know what's going to happen by the time it's over. Alfred's line in the last chapter sums it up:
Alfred: It's just that it's been so many years since I've seen him so... so carefree. I find myself wishing there was a way he wouldn't have to go through it all again.
- In one issue Killer Croc sees a news report where Summer Gleeson wonders on-camera just what the life of someone like Croc must be like. He confronts her and tells her how he's been mistreated, and when she fearfully says she feels sorry for him, he leaves delighted that someone's on his side. Then at the end, as he's fighting and beating Batman and Robin, he sees Summer staring at him in horror and Croc just... shuts down.
- In one short piece, we see Harvey Dent finally be cured of Two-Face by a lovely doctor who repairs his damaged face and psyche. Unfortunately she has a Ax-Crazy twin sister who has the hots for Two-Face. She finally kills her good sister, leaving Harvey wild for revenge. He burns his face and goes back to his madness, killing the evil sister. We then see that he's been telling all this to Batman as he stands behind Harvey, who finishes with: "Now take me back to Arkham. It's where I belong... with the rest of the crazy people."
- There's even one for Scarecrow in the first annual. After having a And Then What? moment, he escapes Arkham and manages to changes his identity, getting a job at a local university, making a Heel–Face Turn as he finds himself teaching a smart female student, who he genuinely likes and is proud of. But all of it comes crashing down when he finds out later that her Jerk Jock of a boyfriend not only beat her, but also possibly raped her too, traumatizing the poor girl. All of this is too much for Crane as this results in him having to go back to the life he tried to escape. But this does also count as a Crowning Moment of Awesome as the first thing he does as Scarecrow is to teach the asshole boyfriend a lesson in fear...
- Of course poor Arnold Wesker, aka the Ventriliquist, gets one. Scarface, thinking Arnold is trying to replace him, goes after the poor guy's family to keep him in line. He threatens his mother in particular, which upsets Arnold more than anything. Batman and Robin catch up with him, only to find that Arnold's family is full of bloodthirsty mobsters, with Arnold's late father as their former leader. By the time they fight their way through them, they discover Arnold sobbing on his knees. turns out Arnold's beloved mother has been dead for twenty-five years, after taking a bullet meant for his father. All he had left to remember her was a picture, which Scarface forced him to destroy.
Arnold: So I shot him in the head. And now my hand really hurts...
- Dubiously canon as it may be, it's hard not to feel sorry for The Ivy plant clone that dies as she desperately tries to regain her humanity.
Tear Jerker / The Batman Adventures
At their best, the Batman Adventures books had tragedy as heart-rending as the animated series that it is based on.