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Jinxie's Mood Matrix segment in Case 2. She's so afraid to recall what she saw at the crime scene that her fear overwhelms all other emotions on the matrix. She starts having a complete and total breakdown and remembers everything in the room as monsters. As Athena points out, your goal isn't so much as cross-examining her as it is giving her therapy.
Juniper Woods breaking down after Apollo's perceiving in Case 3. She really didn't want her role as Professor Courte's class snitch to ruin the friendship between herself, Hugh O'Conner, and Robin Newman, however after she overheard that Hugh O'Conner has bribes for his grades she believed that Hugh himself is making the bribes and not his parents. And yet even after all that he still is willing to take the fall for her? That is true friendship right there.
Hugh, Robin, and Juniper each making false confessions in order to take the fall and protect the other two, knowing that a criminal record means expulsion from Themis Legal Academy.
The UR-1 Incident is basically theDL-6 Incident for Athena Cykes and Simon Blackquill. The former witnessed her mother's murder right in-front of her eyes at age 11, while the latter was falsely convicted for the said murder while trying to protect the girl and is on death row for it. The former is very lucky to even being alive after that because she attacked in self-defense against the real criminal Phantom. It is this incident where "the Dark Age of the Law" came into effect, infecting the wound that had already been opened by Kristoph Gavin's framing of Phoenix.
It gets to the point where Athena is accused of matricide. It really didn't help that Edgeworth, of all people, would suggest that an eleven-year old girl would kill her own mother and try to dismantle her to remove evidence. Then this idea gets worse at the end of Simon's Mood Matrix, when it's revealed what he witnessed when he entered that lab and saw Athena◊. She is covered in blood with Dull Eyes of Unhappiness all while saying this line:
Athena: Something's wrong with mom, so I'm taking her apart to fix her...
Heck, the UR-1 Incident was pretty horrible for everyone involved. In the picture of the first rocket launch, you can see how happy Yuri, Clay, Sol, Metis, and Aura were at that time. Aura and Metis were close as co-workers (and Aura was implied to be in love with Metis) and Metis was working hard to ease her daughter's abilities so that she could have a more normal life. Simon clearly looked up to Metis as his mentor, and seemed to get along with Athena very well. Meanwhile, Clay and Sol obviously had a strong mentor/student relationship and were striving to make it into space. All of them were working hard and full of hopes and dreams for the future. And from this one incident, it all fell apart. Metis died, leaving Aura bitter and cold and Athena horribly traumatized. Simon went to prison and basically lost seven years of his life. Sol was so traumatized by the sabotaged mission that he fell to pieces at the thought of going on another. And Yuri, who we see cares very much for the people working for him, had to deal with it all and then experience the guilt all over when it looked like the same thing would happen seven years later.
Aura'sbreakdown once she realizes Athena is innocent, and she's been hating her for seven years for absolutely no reason.
All these years, hating Athena was the only thing that's kept me going... But what do I do now? Can anybody tell me? How am I supposed to go on?!
On that note, this song is possibly one of the biggest musical Tear Jerkers in the entire series. It perfectly captures that feeling you get when you realise Athena has been a Stepford Smiler all along.
The Wright Anything Agency falling apart starting off with the murder of Apollo's friend Clay Terran, getting worse when Apollo leaves the Agency, gets much worse when one piece of evidence implies that Athena killed Clay Terran, and comes to a head when Apollo indicts Athena for the said murder. He really wants to believe in her which is why he limited his perception ability around her but his doubts eventually led him to said indictment even though he really wants her to be innocent. The location of the murder? The same Space Center that the UR-1 incident occurred.
Apollo's breakdown at the end of the investigation stage in Case 4, just before he takes his leave from the agency. For a guy who's always smiling, seeing him yell out in anger "DAMMIT... IT'S NOT FAIR!!!!!!!!", and Trucy and Athena's shock at his outburst, just brings out the anger that Apollo is feeling after his best friend was murdered. Everyone's worry after Apollo takes his leave of absence is also heartbreaking.
Right before Apollo announces his decision to leave, he talks about his friendship with Clay. His memories are heartwrenchingly bittersweet after Clay's death. "I'm fine! You're fine! We're both fine! Ha ha ha ha ha..."
However, as proof that Tear Jerker moments don't always have to be sad, there's yet another scene in Case 5. Phoenix, possibly for the first time since his second case, finds himself alone at the office. With a clearly-hurting Apollo going off on his own, Trucy having decided to follow him, and Athena having been arrested at the end of Case 4, Phoenix is feeling at his lowest, as he had taken it for granted that they would always be there. Cue a letter from Maya and a surprise visit by Pearl, which end up being exactly what he needs to lift his spirits.
The Bad Endings (most of them on Case 5, Turnabout for Tomorrow):
Fail to get Simon Blackquill on stand? Athena is found guilty by default and Phoenix never sees her again.
Fail on Fulbright's final testimony? Athena and Simon both got off the hook, but Fulbright gets away clean and the failure to find Phantom causes public opinion towards the law to sink even lower.
Fail in one of the two forced questions? Aura kidnaps Athena and you never see her again.
Fail Rimes's Mood Matrix segment in Turnabout Reclaimed? Orla is found guilty in Buckler's place and is put down.
Also in case 5, Aura Blackquill's outburst about her almost certainly romantic feelings for Metis puts the rest of her personality in a new light-one that turns her from a mere Jerk Ass into an outright Tragic Hero. All she had left of Metis was that picture on her desk, and her vengeful hatred of Athena. Goes to show just what the affects of losing someone you deeply care about are.
Not to mention, Ponco tells you how Aura began crying at night after Metis died and refused to let the robots call her "Mama Aura", like they used to.
Case 5 again. The reveal that the phantom is not actually Bobby Fulbright, but just pretending to be Bobby Fulbright can be this. There really was a detective as kind-hearted and morally honest as Bobby Fulbright, but he was killed just so that the Phantom could use his identity as a convenient cover, bastardizing his quest for justice.
Another one for case 5, which is more of a happy example: after being confronted by Blackquill, who expresses his gratitude towards Athena, she breaks down in Tears of Joy. Phoenix's thought helps seal her breaking out of her Stepford Smiler status.
Phoenix: (............Thatta girl, Athena. It's good to see you finally let your tears out.)
Heck, just the fact that, in a first for the series, there isn't a single Asshole Victim to be found among the murder victims of the game, all of them were genuinely nice people. Meaning this is possibly one of the saddest games in the series when you think about it. To wit:
Candice Arme was a dutiful police officer who was suddenly murdered trying to stop Tonate from stealing the bomb evidence.
Rex Kyubi tried to protect a village secret and stay friends with Tenma, it was also implied that L'Belle threatened his hospitalized wife.
Constance Courte tried to teach her students that fair play in court was the only way and fought against Professor Means' philosophy. She was murdered by Means over bribery. As a mentor to Klavier, she falls into Too Good for This Sinful Earth territory, especially with the atmosphere of Themis ensnared by Means' grip, being the sole voice of reason.
Clay Terran was entrusted by Director Cosmos to help stage the rocket swap, to protect both him and Starbuck, who was traumatized by the HAT-1 disaster seven years prior. As Apollo's friend, he helped push Apollo towards his goal as a defense attorney as Apollo helped pushed Clay into becoming an astronaut. He was murdered by Phantom for something he didn't even know he had, namely the moon rock in the Hope capsule. He never got to achieve his dream of going into space.
Metis Cykes was introverted, but loved her daughter Athena with all her heart. She tried to help the child with her inability to tune out emotions, but was seen by Athena as just being part of being used for an experiment. Her murder came at the hand of the Phantom for a psyche profile she no longer had, but her gift to her daughter ultimately helped catch her killer.
You never got to meet the real Bobby Fulbright. However, if Phantom's act was anywhere close to the real deal, then Fulbright was a good man dedicated to justice who was cut down all too soon, for something he never even saw coming.
This also applies to the DLC Case, Turnabout Reclaimed. Both deaths involved in the case were accidental: Azura Summers died of a heart attack from a condition she kept secret from everyone due to not wanting to give up her job as a trainer, and the blame fell on the original Ora who was trying to save her (and later on Orla who was put in the original's place); while Jack Shipley died trying to save Orla from Marlon, who didn't want Jack to die at all. Shipley did some mildly unscrupulous stuff, like using technically illegal monitoring equipment to watch out for his animals and lying about euthanising the first Ora. However, he was otherwise a solid guy through and through (such as wanting to stop Sasha from performing because he learned of her heart condition and not wanting a repeat of the aforementioned trainer's death), and he actually rescued Orla when she was beached, nursing her to health to the point that Orla, when released into the ocean, came back to Jack. It's implied that he let himself fall when Rimes tried to save him, so Rimes wouldn't fall in and die with him.
Following up on that, how about the defendants themselves? Juniper is frail and sickly yet accused of two crimes (both of which would land her for first degree murder charges), Damien Tenma has only his beloved daughter and his going to prison would leave her alone in the world; then there's the last three defendants, all of whom seem to suffer some degree of PTSD linking back to the same incident seven years ago, two of which you have to continue to trigger in order to get the truth out. In the DLC case, the first of the accused can't even speak out to defend herself, and the second puts her with the likes of Juniper due to her medical problems. Usually in the games, there's at least one trial where the defendant isn't a complete woobie. Not so in this one.
Marlon Rimes'Villainous BSOD at the end of Turnabout Reclaimed. Despondent at the discovery that he was trying to kill an orca who was not at all, involved with his girlfriend's death, he refuses to admit that Jack Shipley's death was accidental, instead claiming that he deserves the death penalty. It's only after Phoenix reveals that Marlon had tried to save Shipley's life and Sasha tells him to return to the aquarium after his rehabilitation is the BSOD broken.
A large portion of the last two cases are just horribly depressing by default, especially since it's hot on the tail of what can be the most comedic trial in the series, victim's death aside. Following a hilarious Unsettling Gender-Reveal, Athena trying to turn herself into a bust of Phoenix Wright, and Professor Means' sudden personality shift on top of Simon as the Only Sane Man, we have the brutal murder of Apollo's best friend, the accusation of Sol who was Apollo's hero and friend as well as the accusation of Athena who is Apollo's friend as well, being forced to trigger both Sol and Athena's PTSD, the abduction of Trucy, the entire UR-1 incident and the things that surround it, and an endless list of other depressing things. It's like the writers took the saddest bits of Cases 1-4, 1-5, 2-4, and 3-5 and brought them together in one unholy abomination of sad. In-universe, cases 1, 4, and 5 all happen within just a few hours of each other; Case 4 begins on 16 December, then Case 1 is 17-18 December, and Cases 4 and 5 are 20 December. 15 December to 20 December must have been really, really rough on the characters. It's sad enough in the meta sense.
Huh. It's almost like things weren't ridiculously sad enough for everybody, so they had to set a supposed case of matricide four days before Christmas. Or rather, four days before the 26th anniversary of DL-6. And yeah, of course that's the exact case that Edgeworth comes back to prosecute.
One more for Case 5: Apollo on the witness stand. Unable to accept Athena's innocence so easily, he takes the stand accusing Athena of murder while emulating his first mentor Kristoph Gavin, just so that Phoenix can find some hole in his logic and let him believe in his friend's innocence.
Apollo: You're just bluffing again, aren't you?......It's fine, Mr. Wright...Even a bluff would suit me just fine...As long as you can...clear up this doubt inside me!
Apollo's not done yet. Clonco calls him "Mr Terran", since Apollo is wearing Clay's jacket. By this point, Apollo's largely shut out his feelings and has no visible reaction to this at all. It's heartbreaking because Apollo clearly forms rather deep bonds with people soon after meeting them and is quite emotional (he'd known Trucy for how long exactly before he was in tears at the idea of her being abducted by a Knife Nut kidnapper back in his own game?). His best friend of more than ten years being murdered doesn't cause him visible anguish; he shuts down, except when he can't keep them bottled any longer and he lashes out at people.
Solomon Starbuck lapses back into a dejected mood when recalling that upon Athena's arrest, as she was being led to the detention center, she still had to flash a smile and congratulate Solomon on getting off despite the fact she couldn't hide how much she had been crying on the ride over. The whole mood of the beginning of case 5 is just nothing but dead air and really sad feelings.