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4x 01 Pax Penguina
- The utter psychological torment poor Jonathan Crane undergoes at the hands of his kidnappers, especially considering the fact that he's only a bit older than Bruce. Is it any wonder the poor kid snaps?
4x 04 The Demon's Head
- Penguin and Riddler's confrontation after Ed is unfrozen. Ed's confusion and fear from his brain damage can be really hard to watch, and it's obvious both of them somewhat regret the way things went between them, but it's too late to change anything. It's heartbreaking that these two people who used to care about each other so much have reached a point where they have nothing left to say to each other and simply go their separate ways.
4x 08 Stop Hitting Yourself
4x 09 Let Them Eat Pie
- Despite never really trusting her, it's clear that Penguin wanted to give Sofia a chance, especially with how cripplingly lonely he seems and how desperate he is to have just one real friend. When Martin confirms that Sofia has been working with Gordon against him, Oswald is left crying in his car, heartbroken that his suspicions were correct.
4x 10 Things That Go Boom
4x 11 Queen Takes Knight
- At Carmine Falcone's funeral, Zsasz is seen very clearly grieving for Falcone's death. During the Wake, he goes to Falcone's coffin, ejects a single bullet from his gun, and tucks it into Falcone's lapel as a last goodbye, before turning and stalking out of the chapel without a word.
- Alfred has been trying to get Bruce over Ra's Al-Ghul, going so far as to almost "kidnap" him to the chalet in Switzerland. When their tussle goes too far, Alfred knows it and tries to make up with him. Bruce's reaction: Filing emancipation papers with his lawyer and firing Alfred, threatening to show the police his injuries if Alfred doesn't leave.
4x 13 A Beautiful Darkness
4x 15 The Sinking Ship, the Grand Applause
- Samson has a man brutally beaten up, then guns him down right in front of his crying wife and daughter. Indeed, this guy is one heartless bastard.
4x 16 One of My Three Soups
- Jerome did not have a happy childhood. One of his recollections involves his uncle sticking his hand in a boiling pot of chicken broth for stealing a cookie.
- Particularly noteworthy was his honest astonishment that Bruce would try to save him from his abusive uncle, which leads to a rare pet the dog moment where he tries to save Bruce. "No one ever tried to help me. Which begs the question, what's wrong with you?" There's also his comment to his (now dead) uncle that he "really brought back the utter helplessness of childhood."
- Jerome's uncle gains the upper hand and prepares to pour a bowl of boiling hot soup down his nephew's throat, it's the only time in the series we see Jerome look genuinely afraid.
- In a subdued way, Jim and Harvey's conversation at the end of the episode: "No heroes here." You can tell both men regret many of their past actions that lead them to say that.
4x 18 That's Entertainment
- One for the fans: Jerome died. Again. Cue the angry tears.
- Blink and you'll miss it, but Jeremiah actually seems a bit upset when he sees Jerome's body. Despite how terrified he was of Jerome, they were still twins, and he probably didn't want his brother to die.
- For a brief moment, Bruce Wayne seems poised to make a connection with Jeremiah Valeska, even complimenting his mind and offering to work together with him through Wayne Enterprises. Just a small example of what could have been, as Jeremiah goes home and is promptly doused with a very special laughing toxin.... It seems highly probable that the next time he and Bruce see each other, they'll become mortal enemies.
4x 20 That Old Corpse
- Bruce's obvious heartbreak at Jeremiah's betrayal, followed by his reaction to Gordon's supposed death.
- The conversation between Jim and Lee in the interrogation room. It's painfully obvious that they still care about each other, but his morals won't let him let her go, and she's too jaded to back down. It ends with her desperately insisting that Jim join her in the Narrows.
4x 21 One Bad Day
4x 22 No Man's Land
- Butch's condition is finally cured and he honestly calls Oswald his friend, saying that he'll be there if the other man needs him. Oswald calls Butch his friend too and apologizes, before shooting Butch in front of Tabitha and killing him. Oswald reminds her that she killed his mother and he has lived with that pain everyday. He wanted her to suffer like he did, to watch as someone she loves die right in front of her and be unable to do anything about it. Oswald then shoots her in the leg and promises that when he's decided that she's suffered enough, he'll kill her.
- After Tabitha is hauled away, Oswald looks back at Butch's body with a clear look of remorse. It's obvious that when he said he was truly sorry, he really meant it. After all, he did just gun down a man who sincerely called him a friend just a few moments prior.
- Especially heartbreaking because even Gotham's revolving-door approach to character death isn't something Tabitha can hope for, in Butch's case: he's already experienced a resurrection and loathed what it made him, so even if she bribed or coerced Hugo Strange into reviving Butch again, Butch would probably never forgive her for putting him through that, a second time.
- Even if he is somehow brought back to life in season 5, he'll have to live knowing that Tabitha is dead. Stabbed by his friend Penguin. And if he'll be willing to put her through all that.
- Bruce tearfully promises Selina that he'll stay with her at the hospital, only to be forced to break that promise: first by the military, then by his kidnappers, and finally by his own greater obligation to Gotham.