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Tear Jerker: Batman Beyond
In the pilot "Rebirth," after much silence, Terry finally breaks down after his father's death.
Bruce Wayne's last fight as Batman in the same episode. The fact that Wayne struggles to keep up with the goons and eventually resorts to using the same weapon that killed his parents makes it all the more depressing. One could see why he retired after that.
The fact that Batman, due to his advanced age and heart problems, was willing to compromise his one rule to save the child of Veronica Vreeland, one of his few remaining friends from BTAS, possibly makes this worse.
"Speak No Evil" has this exchange:
Fingers: You want to put me in a cage again?
Batman: Well, yeah.
Fingers: You're all alike—you, the doctors, Van Dyle.
Batman: Who's Van Dyle?
Fingers: You have a mother?
Fingers: I don't because of Van Dyle.
"Meltdown": Freeze's swan song episode.
His last words: "Believe me. You're the only one who cares." No, he's not, Freeze. He's not.
Terry's utterly heartbroken "Oh, Fries..." when it became apparent that Victor returned to his old ways. Mostly because, as the above quote says, Terry was the only one who had any faith in him.
The climax of "Dead Man's Hand" where Melanie's father orders her to come save him just as a security guard shows up. Terry whispers: "Don't do it. Just go" with the most heartbreaking voice and facial expression. The scene of him watching the police take her away is also just as devastating because just as she's in the back of the truck, Melanie sees Terry in the crowd.
Near the end of the episode, when Ten is shot at and starts to fall, Batman catches her as she looks at him remorsefully, saying, "I don't suppose I could convince you to let me go." We're then treated to a somber Kubrick Stare from Batman, which says a lot with only one expression, seen here◊.
"Earth Mover" is riddled with heartache. You have a man buried alive in radioactive waste seeking vengeance on his business partner who raised his daughter in light of the accident. He gets a Face-Heel Turn when he uses the last bits of his life to allow them to escape with a heart-wrenched "Jackie."
"Out of the Past"
The final line:
Bruce: Rest well, beloved.
Earlier in the episode, Bruce looks over some pictures of his more notable relationships. It's sad because he realizes how much time has gone by and just how alone he is.
In a cross-media example, Superman/Batman Annual #4 is a continuation of "The Call," which has Superman dealing with everything that happened while he was under Starro's control, including Lois' death.
Terry and Bruce's fight in the Justice League Unlimited episode "Epilogue" and especially the part where Bruce is struggling for his pills while Terry, instead of helping, just stands and watches in disgust. He tells Bruce he is insane and leaves him on the floor struggling for his meds while he is having an attack. Considering how close Terry and Bruce were on the show, seeing their relationship come to this is really hard to watch. Thankfully that scene was just a potential scenario in Terry's mind and not what actually happened. Still a horrible thing to watch.
In the same episode, we find out Ace (in a flashback) died of an aneurysm caused by years of experimentation on her. Not only that, but her last request was for Batman to stay with her until the end, since both of them had their childhood taken away.
"Disappearing Inque." Bruce has donned the exosuit to save Terry from Inque. Terry looks on in shock and terror. The exosuit puts such a strain on Bruce that he could very well die.
Made even more heartbreaking when you stop and think about what happened the last time Bruce's protege was kidnapped by a dangerous supervillain, as revealed in Return of the Joker. Tim Drake ended up severely messed up because Bruce let him fight crime on the streets, and swore off ever allowing another young partner to do the same. He lets Terry don the Batsuit, and Terry is kidnapped and hauled off someplace Bruce can't identify? Bruce must have been kicking himself over that one....
Ace's backstory in "Ace in the Hole," and Bruce's efforts to keep up appearances while he's missing.
Bruce: Don't worry, boy. I won't ever let anyone hurt you ever again.
While it flagrantly contradicts Return of the Joker, the ending of the Hush Beyond comic. Hush is defeated, and Bruce starts talking much more than he normally would, inviting Dick Grayson to come back to the mansion with Terry, even saying that while he knows things can't ever be the same again, maybe this is just a chance for them to speak again...only for Terry to reveal Dick had already walked away and wasn't listening.
The part of "Revenant" where Matt says he wants to hold a seance because he doesn't want to forget his dad. Terry and Mary exchange a look of despair, and ultimately Mary has to say that ghosts aren't real.
"Mind Games." A lost girl named Tamara frantically calls Terry for help. He's forced to use every ounce of his (and Bruce's) detective abilities to find Tamara and every ounce of his combat abilities to fight the super-psykers who abducted her, all while comforting her to the best of his ability.
In that same episode, Terry and Bruce flip through pictures of missing children to see if Terry recognizes one of them. Many pictures appear onscreen, only of young girls. Terry is obviously shaken by it.
"Betrayal." The whole episode is pretty depressing with Terry feeling responsible for his old friend Charlie turning into the mutant "Big Time" and returning to a life of crime. Terry tries to convince Charlie to leave his gang and turn himself into the cops; it looks like he's finally gotten through to him, but when the gang gets taken down by the police, Charlie reveals that he had no intention of turning himself in or getting cured, and he was only using Terry to get rid of the gang so he could start his own criminal empire. Then to top it off, he tries to kill Terry in spite of everything he's done to try and help him and, after a fight on the bridge, Charlie ends up falling to his death and Terry just stares sadly and Bruce tries to comfort him over it and relates his own fallout with Dick Grayson and/or Harvey Dent becoming Two-Face.
Bruce: I'm sorry. I know how hard it is to go against a friend.
Terry: I outgrew him, that's all.
The theory of Warren and Mary's divorce being caused by Warren suspecting Mary of infidelity, due to the boys' black hair and blue eyes. They are still married when Terry is about eight, implying that Warren forgave Mary for the first time, and they divorced after Matt was born. The real kicker is that Mary was never unfaithful to Warren. The boy's true parentage was due to Warren's reproductive material being overwritten with Bruce Wayne's with what he thought was a flu jab, as a secret unsanctioned government attempt to create a new Batman. So he essentially suspected Mary of having an affair with a man she'd never even met. Their marriage was essentially ruined by an outside party, yet they were still on good terms with each other in a platonic sense and treated both Terry and Matt with mutual love and respect.
The reveal of Payback's identity as the counselor's son who thought that getting rid of the teenager's tormentors would allow his father to spend more time with him.
In the "10,000 Clowns" arc of the digital first comic, Bruce is trying to re-establish his relationships with Barbara, Tim and Dick. He's doing his best to develop a working relationship with Commissioner Gordon; he bribes Tim to work at Wayne-Powers by doubling his current salary and promising to put his kids through college; and the previously-mentioned appeal to get Dick just to talk to him. But Dick does not, and after Terry guilt-trips Tim into going down into the Batcave and helping him stop Joker Night, Tim is so upset by the experience that he quits the job. A year later, Terry is working with Dick instead of Bruce, and Bruce is apparently entirely alone again, with just Ace.
In Batman Beyond 2.0 Terry is (seemingly) killed by Lord Superman in the middle of telling his alternate-self to tell his version of their family he loved them and Alternate!Dick is the one ordered to make sure his corpse is strung up to send a message.