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3x 1 Better to Reign in Hell
- After his grand exit to find Lee last season, Gordon discovers she's already moved on with someone else during the months apart from him. He apparently doesn't even talk to her, not wanting to disrupt her happy new life.
- Selina giving Bruce the cold shoulder, because he left town without bothering to tell her (again) which understandably pissed her off.
- Selina's reaction when Ivy is seemingly killed, and being helpless to stop it.
3x 2 Burn the Witch
- When Penguin is crying in the woods after letting Fish go, it's easy to see that he's still deeply heartbroken over his mother's death.
- Bruce's devastation after being forced by the Court of Owls to give up his quest, in order to spare the lives of the people he cares about. He almost breaks down sobbing in Alfred's arms.
- Ivy's confusion after surviving Marv's attack. You can see it especially when the man who helps her asks about her: "Cops killed my dad. My mom left. I was alone, abandoned. But then... something happened. I changed. Grew. I'm different. Inside and out."
3x 3 Look into My Eyes
3x 4 New Day Rising
- Crossing over into Nightmare Fuel, what Jervis did to his sister. As a sick game, he would put thoughts into Alice's head that "no brother should ever have", a not-so-subtle reference to incest. That's right: he sexually assaulted his own sister for years with actual Mind Rape! You can just see Alice cracking inside as she's forced to recount what he did, and later, when he finally captures her, she's trembling and crying and trying so hard to be brave, and you can just see what he did to her her whole life. It makes her death even more heart-wrenching: she never got to have a life away from his monstrous abuse.
3x 5 Anything For You
- Penguin talking to the statue of his mother makes it clear how much he loved her and how devastated he still is over losing her.
- Even though Selina doesn't yet know that the snobbish redhead is Ivy, it still hurts when Ivy treats Selina badly. Especially when you consider how Selina had previously been her only friend, and how many friends Selina has lost or how many times she has been betrayed over the series.
- The conversation between Selina and Bruce on the roof contains several tearjerkers: Selina's standoffishness towards Bruce is notable because she might still be hurting from their difficult startups this season - Bruce leaving for so long, and then his (initial) refusal to help look for Ivy. It could also be a sign of how much they both have been through in their young lives and what a toll it's taken on both of them, especially Selina. You can see the pain and weariness in her eyes in response to Bruce's determination.
Bruce: "I feel something, and I know you do too. We're the same."
Selina: "In what universe are we the same?!"
Bruce: "The money doesn't matter!"
Selina: "Try not having it! It matters."
- The scene were Edward was unconscious after Butch nearly strangled him to death. You can hear the terror in Penguin's voice as he practically begged his friend to wake up. Almost every person he cares about dies in his arms like his mother and father, and he didn't want to go through that again with Ed.
3x 6 Follow the White Rabbit
- During the Mad Hatter's tea party, Gordon tries to goad Jervis into killing him instead of Lee or Valerie by telling him that Alice hated him, saying that she died rather than be with him. Jervis' attempts to convince himself otherwise devolves him into a quiet, Rapid-Fire "No!". He's so deluded that he actually believes his love for his sister was normal. And when he attempts to shoot Gordon, he's close to tears.
- When the Mad Hatter gives Gordon the Sadistic Choice of killing either Lee or Valerie, ultimately, he chooses Lee, much to her shock and horror. After concluding that Gordon loves Valerie more because of this decision, Tetch shoots her instead, and she's immediately rushed to the hospital while Tetch makes a clean escape. When Gordon meets with Lee afterwards to explain his decision, she coldly tells him not to talk about it. The episode ends with the two of them sitting side by side, in cold, bitter silence, before the ending title screen quietly caps off the episode. It's obvious he still hasn't gotten over his breakup with Lee.
- Ed misses the romantic dinner where Oswald intended to profess his love because he runs into a Kristen Kringle lookalike who speaks riddles.
3x 7 Red Queen
- Valerie won't be lied to. When Jim tries to tell her that he didn't mean for her to get shot, she tells him he meant to save Lee, and then breaks up with him. The realization that, whichever woman he chose, he actively chose for one of them to get shot, and the silent tears rolling down Valerie's face, just hammer it in what a hurtful situation Jervis put them all in, emotionally as well as life-threatening.
- Jim's hallucination of Leslie and the family they never got to have, as well as losing them one by one.
- The final conversation Jim has with Barbara's hallucination. Even more so if Jim and Real!Barbara actually feel this way and could have had a conversation like this in real time:
Hallucination!Barbara: "Don't be scared. It's not easy to face who you really are. I should know."
Jim: "Do you ever wish you were the person you used to be?"
Hallucination!Barbara: "Do you?" [Both exchange a sad look.]
- Barnes has apparently accepted his apparent demise from Alice's blood, having typed up his Will and making his final arrangements.
3x 8 Blood Rush
- Barnes' final days before the virus consumes him. After losing his temper and killing a criminal, he forces himself to make it right and goes through the episode like a man living his last day. He brings in the man responsible for the murder he walked in on, tells Jim how glad he is to see him with a badge again, and leaves work early to wish Lee well on her engagement party, spending time around people he cares about, fully resolved to turn himself in for his crimes. But before he can bring himself to do it, he snaps one final time at the sight of the man he arrested walking free, kills him, and gives in to the virus entirely.
3x 09 The Executioner
- Whether or not you feel bad for Isabella as a blatant plot device, Ed's subsequent reaction to her death is still rather tear-inducing. Especially when the friend he goes to for comfort is lying to his face.
3x 10 Time Bomb
- Jim and Lee's conversation at the end of the episode is just so...melancholy. It's clear just how much they meant to each other and how disappointed they are with how their relationship ended. All they can do is have a kiss goodbye...
3x 11 Beware the Green-Eyed Monster
- Jim reveals to Lee that he still loves her, he never stopped, and should have told her sooner. He tells her that he went to see her after the Arkham incident, but he saw how happy she was with someone else (Mario) he didn't want to ruin it. Lee tells him after the wedding, they leave Gotham and never return. Then Lee breaks into tears as she slaps Jim, angrily scolds him for not only making "wild accusations" on Mario, but for telling her too late he still had feelings for her on her wedding.
- Ed's reaction to finding out that Oswald had Isabella murdered. Oswald is his best friend, arguably the only person he'd do anything for, and he went behind his back for an entirely selfish reason. This is doubly worse with the fact that Ed basically loses the only two people he loved, one to death and one to betrayal, and one at the hands of the other. It's almost impossible not to feel for the poor guy.
3x 12 Ghosts
- Just the fact that the kind and loving Elijah van Dahl has been horribly removed from his grave and is now being used to psychologically torment his only son. While Oswald arguably had it coming, Elijah certainly didn't. And it's later mentioned that his body was unceremoniously thrown into a dumpster behind a Chinese restaurant. Bonus points for Oswald's face when he finds out.
- Fridge Sadness: Ed and Oswald's first friendship moment was eating Chinese food together in Ed's apartment. Nygma really went out of his way to taint the memory of every good thing they had together.
3x 13 Smile Like You Mean It
- Selina is heartbroken when she discovers that her mother saw her as an easy mark and only came back to Gotham to take advantage of her daughter dating billionaire Bruce Wayne. That her mother gave Selina her baby things last episode and seemed set to bond with her daughter only makes the betrayal even deeper for Selina. Then she discovers her boyfriend had suspicions about it but never voiced them to her. By the end of the episode, Selina is in tears and feels betrayed by the two people she cared for the most.
- Which is especially harsh, considering she's already more-or-less lost her two best female friends in the last few months: Bridgit, to Strange's mind-meddling, and Ivy, to her aged-up condition making her more like a stranger than the kid Selina used to protect.
- In spite of the many bad choices he's made, one might feel sorry for Gordon when Lee makes cutting comments, accusing him of wanting to kill Mario. Considering that Gordon only narrowly saved her from her new husband murdering her on their wedding night, it seems like a very unfair accusation. You can just see the sadness in Gordon's eyes that the woman he still loves hates him so much, and also that her pain is killing him to watch.
3x 14 The Gentle Art of Making Enemies
- For all he deserves it, Oswald is really put through the wringer in this episode, and it can be quite hard to watch the powerful and charismatic Penguin suffer and ultimately emotionally break.
- The look on Ed's face when he says "The truth is, Oswald, that you would sacrifice anyone to save your own neck. Even me." Beneath his anger and desire for revenge, and sadness at losing Isabella, Ed's also just plain hurt by Oswald, from his perspective, betraying him.
- Whether or not his revenge is Disproportionate Retribution is up to you, but the whole situation is still unbelievably tragic from Ed's perspective. His best friend, someone he thought accepted and cared for him wholeheartedly, and that he trusted and idolized in return, turns on him for an incredibly selfish reason, and then lies about it in an attempt to keep and control him. Given that everyone else he's ever known has (in his twisted mind) let him down, it's easy to see that Ed honestly believes Oswald never really cared about him and was just using him the whole time. Is it any wonder he lashes out in such a manner? The way Oswald can only tearfully shake his head in denial makes the whole thing worse.
- And then when Oswald won't sell him out, even to save himself, Ed is incredibly shaken. It's like all his anger drains away as he's confronted with the fact that as misguided as Oswald is, he really does care about him, and Ed spends the rest of the episode obviously conflicted. It's just heartbreaking that in order to give Isabella justice, Ed feels like he has to gun down a man who would do anything for him, arguably the only person left in his life that cares about him, and it's obviously eating Ed up inside. Even as he goes through with it, it's clear he's taking no pleasure in it like he was earlier in the episode.
- The look of pure betrayal and disbelief on Oswald's face when Nygma shoots him. He just can't believe what is happening; the confident and clever Penguin, who's always talked his way out of these situations before, is utterly lost for words. He just silently stares at his best friend and love interest, heartbroken.
- Despite his legitimate anger and desire for revenge against Oswald, Ed's face when he shoots him is far from triumph; it's a mix of horror, relief, sorrow, and even guilt. You can practically hear him thinking "What have I done?"
3x 15 How the Riddler Got His Name
- The revelation that, despite the events of the last episode, Edward still misses Oswald dearly, and has since become a mental and emotional wreck that resorts to taking hallucinatory pills in order to keep an imaginary Oswald around him for a bit. At the end, when Nygma finally becomes the Riddler, he bids Hallucination!Oswald farewell, and throws away the pills to cement his best friend's parting. Little does he know, Oswald is still very much alive, and is now bent on murdering his former companion...
Ed: I admit that - that killing you killed a part of me! But I will find a way forward, no matter the cost...
- Ed's obvious guilt throughout the episode. When Lucius confronts him about what happened to Oswald, Ed is so upset he actually messes up one of his riddles, shaking his head and turning away like a little kid in denial, and covering his eyes. In the car, his voice breaks when he says that he killed him, and it's obvious how hard it is for him to even force the words out. Eddie is so devastated by his best friend's apparent death that he can't even acknowledge what he did until the end.
Ed: I just - killed the best friend I have ever had. My search for a teacher, or an enemy...that was just me trying to hold on to him a little longer...
3x 17 The Primal Riddle
- Jim and Ed reminiscing about the double-date dinner they had with Lee and Kristen is rather sweet, but also quite melancholy; it's a harrowing reminder of how far they've both come, with even Jim admitting it feels like a lifetime ago. Kristen is dead, Jim and Lee are estranged, and Ed has slipped irrevocably into evil...but he can still recall the exact details of the meal and Kristen's outfit, and it's obviously a memory both men still treasure deeply. What really brings on the waterworks though is Jim quietly admitting that he had a good time and that he considered Ed his friend. And then Ed coldly responds that every friendship ends in betrayal, so what good are friends anyway. It's a sad reminder of how far he's come from the man that wanted so desperately to be accepted, but why wouldn't he think that? Both men that he considered his friends, Jim and Penguin, have (in his mind) turned on him.
- On a similar note, Oswald returning to the Van Dahl manor and seeing the vandalized painting, along with the news report on Ed. He doesn't say anything, but the pain on his face clearly communicates that beneath his anger and desire for revenge, he's still just plain hurt by Ed's betrayal. Neither of them have gotten over their friendship falling apart, however much they might claim otherwise.
3x 18 Light the Wick
- Ivy's desperation to bring Selina back to after being told by the doctors that Selina's case was 'hopeless'. Taken to the next level when you recall that Selina is, and always has been, Ivy's Only Friend.
3x 21 Destiny Calling
- The cruel (permanent) death of Fish Mooney, unceremoniously stabbed in the gut by a virus-infected Jim Gordon. Much like Gertrud Kapelput, she then dies in the arms of a heartbroken Oswald while he tearfully promises that he'll get her help. It's doubly sad that this powerful woman who beat death once before hardly had a chance to defend herself this time.
Oswald: "It's ok, we can get you some help -"
Fish: "No no no, I've done this enough times to know I'm finished."
Oswald: "No - do not say that, we will get you help!"
Fish: "Listen to me. You make this city yours...or you burn it to the ground."
- It's even worse with the realization that despite all they'd done to each other previously, Fish was basically the only person Oswald had left at this point.
- Alfred's willingness to die for Bruce, which doubles as heartwarming.
3x 22 Heavydirtysoul
- Selina comes to the hospital to see if Alfred is OK after Bruce stabbed him with a sword. Bruce tells Selina that he doesn't want her there and then says that she doesn't care about anyone but herself. You can clearly tell that this hurts Selina; she says in a soft voice that she thought Bruce did know who she was. Considering that she came to Wayne Manor a couple episodes ago to kill clone!Bruce and warn Alfred about Bruce being missing and the impending danger to Gotham, and considering that she was there in the hospital to see if Alfred was OK, it's clear that she does care. But the latest rejection from Bruce is too much for her. Before she lets out her anger, telling Bruce to "have a nice life", you can see how hurt she is by his attitude towards her.