Arven's desperate quest to help his Mabosstiff recover from an injury so serious that neither Pokémon Centers or any kind of medicine have had any effect. The poor thing can't even see, talk or stand in its current state. The epilogue to the fifth Titan battle hits the hardest — Arven is on the verge of despair when it seems like not even all five kinds of Herba Mystica were enough to save his best friend, spending the last few moments before he loses what little hope he has left begging him to get better so they can play together like they used to. Thankfully, Arven's quest did pay off, but still.
This hits harder when you investigate various things in the lab and Area Zero. There's a pet bed in the lab in the lighthouse that has "Maschiff" written on it in kid's handwriting, and in Area Zero, there's a photo of a young boy and his Maschiff. That means that Arven's Mabosstiff was basically the only consistent affection he received for the majority of his childhood, given that one of his parents left and the other threw themselves into their work to the point of neglecting him.
Given that Arven later learns that his remaining parent is dead, imagine how much more devastating the ending to "The Way Home" would be if Mabosstiff had died too. The fact that he makes a full recovery almost feels like the game's preemptively apologizing for what it's about to put Arven through.
The "emotional" music themes written for this game, in particular "Arven and Mabosstiff" and "Mabosstiff's Recovery" have generally been regarded as some of the saddest songs in the entire franchise, up there with N's themes from Black and White.
A small but still painful moment happens near the end of Path of Legends. After the player and Arven get the last Herba Mystica and Sada/Turo contacts the protagonist for updates on Koraidon/Miraidon, Arven comments that he hasn't actually heard his parent's voice in a long time. He initially feels annoyed that Sada/Turo wants him to bring the player character to the lab, feeling like his parent is just making him run errands after they haven't seen each other in a while. Still, he goes ahead to the lighthouse anyway and tells you to come along. It shows how badly he was affected by his Parental Neglect while also wanting things to be normal again.
The story behind Team Star's founding: it's members were aggressively bullied at school and they formed a group to protect themselves and each other, only to end up becoming just as bad as their bullies. To anyone who's been bullied for whatever reason, especially if they've been consumed by hatred and corrupted as a result, it really hits home. Luckily, at the end of the story, Clavell gives them an Unishment by having them repurpose their facilities as training facilities.
Especially Penny, who at one point states that her anxiety of being bullied was so severe she couldn't bring herself to go to school for a long time.
And of course ... they weren't nearly as bad as the bullies, that was just the outgoing deputy director covering things up.
A small group of former Star Grunts has gathered in one area, having quit the group, but not returned to the Academy. One of these NPCs off-handedly mentions that "No one fights" there, describing it as being better than the school, better than being with Team Star... and "better than home", which has some uncomfortable implications.
Beating Eri of Team Star's Caph Squad—the final Team Star Boss before the "Big Boss", results in her not only dropping to her knees after losing the battle, but after giving you the boss’ badge, she asks you to turn around as it's too much for her...then she runs off crying.
She can be later seen still sobbing with her back turned, after her friend you previously battled at the gates shares their backstory.
Don't even try stopping yourself from feeling bad for Poppy when you defeat her in your battle with her. The fact that she's upset that you beat Rika (who she looks up to like a big sister) and she couldn't make up for it to the point where she starts bawling once you win is absolutely painful in hindsight.
While initially Played for Laughs when saying "no" to Nemona when she asks the player to be best rivals for life with her near the end of "Victory Road", seeing her increasingly crestfallen expressions as she continues asking until saying "yes" can be a bit painful to witness to the looping point that she resorts to desperate begging Buffy Speak. Especially with hindsight from post-game upon learning that Nemona was basically Lonely at the Top, scaring away her peers with her aggressive desire for battling combined with her established Champion rank, before the protagonist came into her life. There is also her mentioning that her parents were hands-off in raising her while exploring Area Zero for the first time, but not to the extreme Parental Neglect that Arven experienced. These factors combined may explain why she comes off as obsessive and clingy towards the protagonist as she may not have had a real friend prior and would not know proper social behavior because of it, relating to them the only way she knows how and making something special for herself to treasure in return. Hence, making the protagonist her "greatest treasure".
After the team reaches the Zero Lab at the very bottom of Area Zero, they are confronted by a second Koraidon/Miraidon who promptly intimidates your 'raidon into submission once again before they suddenly choose to go inside the Zero Lab. Inside, after meeting the professor, said violent 'raidon shows up again before being recalled by the professor, and throughout the scene your 'raidon looks very much the pitiful Shrinking Violet cowering in fear.
The final act. So, so much of it is bound to emotionally destroy you.
The revelation that Professor Sada/Turo is actually an AI and that the actual professor died protecting the player's Koraidon/Miraidon from a grave accident before the events of the game, as they force you to fight them in order to save the time machine from breaking.
Just before the final battle, it's clear that this isn't one of the fun mutual Pokémon battles you've been having throughout this whole game. The player character doesn't want to fight, and the AI clearly doesn't want to fight either. But as the defense systems override the AI's personality, they're forced to engage you in battle against their own will. And it's shown by the fact that they don't challenge the player, but initiate a battle.
AI Sada/Turo: Please. Defeat me. AI Sada/Turo has initiated a battle!
There's a Freeze-Frame Bonus when the text glitches out after the Paradise Protection Protocol takes over for the second battle, really underscoring just how tragic the AI Professor's situation and lack of free will really is.
AI Sada/Turo has no intention of fighting any more!
The AI themself is tragic in their own right, being a fully-sentient individual that Grew Beyond Their Programming and realized the dangers of their creator’s project but are powerless to stop the time machine without outside help. Due to their existence being tied to the time machine and the crystals in Area Zero, they are also unable to physically leave the lab at all, and later confess to envying the freedom of the player and their friends. To top it all off, they retain the memories of Sada/Turo, but are very much aware that they are not an exact copy, and can only pass on the word that Arven’s real parent loved him long after they’ve already died.
Poor, POOR Arven. He's been all alone with only his Mabosstiff as family throughout his entire childhood... And now he's told that his parent has been deadall this time, created a time machine that could've potentially destroyed the whole world, AND that the he and the player have been talking to an AI copy of them this whole time. He does finally get confirmation from the AI that his parent did indeed love him from the start... just before the AI's Heroic Sacrifice to save the world. To summarize, the poor boy basically has to experience the figurative and literal death of his parent three times, leaving him a scared and depressed kid with no parents left to support him.
AI Sada/Turo: [...]I inherited all the thoughts and wishes of the professor, and so I understand better than any... Your mother/father truly loved you. Arven:(distraught) You...you can't... You can't just go and say a thing like that now!
The AI professor even admits that it's fair for Arven to be upset at them for saying that, driving in just how hard it's hitting him.
The worst part is that Arven admits that he suspected his parent died, but was in denial.
Nemona: Arven... You OK, bud? Arven:(quietly) Yeah. Somewhere deep down, I... kind of already knew it. I knew that thing was fake... but it... When it said my name, using her/his voice and wearing her/his face... Even if it was fake, it... felt real, you know. And so I just... I... (closes his eyes and shakes his head) Sorry... I don't know what I'm saying... Penny: That's... That's OK.
Area Zero in general borders between being unsettling and just...tragic. Between the whole area being shrouded under mist, casting an almost ethereal glow upon the whole area, the wandering Pokémon both of the regular and Paradox variety, the only signs of human life being the abandoned and crumbling outposts, and the awesome-yet-melancholy techno theme (which persists at a higher intensity even in battle), the whole location seems displaced from time itself (which, given what rests in its depths, is somewhat understandable) and even at a glance the whole of Area Zero just seems to scream, "Something terrible happened here."
The fourth research station in particular is a good mix of Tear Jerker and Nightmare Fuel. The first three have plants growing on the outside and clearly haven't been used in a long time, but they're in okay shape otherwise. The last one has visible damage on the outside, before you even go in, with a section of the wall ripped off and lying on the ground in front of it. And then you go inside and see just how bad it is...
The Teal Mask
Ogerpon's backstory. She and her human companion came to Kitakami from a distant land, but were shunned for their strange appearances. A lone mask maker — Kieran and Carmine's ancestor — took pity on them and made masks for them, which made the people like them a lot more. But then, Okidogi, Munkidori and Fezandipiti found out and stole three of the masks. In a rage, Ogerpon donned her sole remaining mask and killed the trio... only to frighten the townspeople into thinking she was an evil ogre harming three innocent Pokemon. From that day forward, Ogerpon was shunned as a monster while the villainous trio were hailed as heroes who "sacrificed themselves" to protect the village. Thankfully, she gets the recognition she deserves at the end while Okidogi, Munkidori and Fezandipiti are shunned by the villagers.
Kieran really gets put through the wringer through the DLC's story. He's already incredibly shy when you first meet him and he almost immediately gets attached to the player character, but once you and Carmine encounter Ogerpon the first time, things only go downhill for him. He believes you and Carmine are mocking him behind his back once he figures out the latter was hiding the encounter from him, he repeatedly loses battles against you and berates himself for not being strong enough, and once Ogerpon's reputation is restored and she allows you to catch her, Kieran seems crushed that the Pokémon he's admired for so long chooses the player over him. After you beat him in one last battle over who gets to catch Ogerpon, he downright breaks, running home to seclude himself in his room and obsessing over needing to 'get stronger' in the last cutscene. Even the player looks worried after finding he's not present for Briar and Carmine's goodbyes.
The tragic dynamic between the player and Kieran. Both genuinely bond over the first day of the trip. However, after the player encounters Ogerpon, the relationship starts to crumble as Kieran starts thinking that the player is making fun of him behind his back with his sister. The straw that breaks the camel's back is ultimately Ogerpon choosing the player as her trainer instead of Kieran. The ending scene with Kieran muttering about getting stronger than the player indicates that the friendship is shattered completely. This entire experience actually makes you feel like Nemona and makes you feel just as alienated as she did when trying to make friends.
This goes even further when you send out Ogerpon against him in their battle at Blueberry Academy, not being able to be her trainer is one thing, having to fight her by someone he hated takes on a whole new level as all his Pokémon will target Ogerpon.
An early sign of Kieran's descent is in the third photo the player character takes. They still try to look cheerful (but even then, their expression looks a bit forced), but Kieran is standing off to the side and just looks over at them with a very awkward/uncomfortable look on his face. It really shows how hurt he is by the player and Carmine hiding things from him.
The Indigo Disk
The state of the League Club with Kieran as Champion. Everybody used to have fun being there, but Kieran's competitive attitude and desire to be stronger has brought down the mood of the club. The player witnesses Kieran's new attitude when he decides to kick out one of his club members for failing to train his Pokémon due to troubles at home. When you consider how sympathetic he was to Ogerpon for how she was treated, it’s so jarring to see him be so cold to someone who has a genuine reason for why he's struggling. It's no wonder why Drayton ropes you into joining the club: none of the Elite Four would have treated that member with such contempt.
When you beat Kieran and become Blueberry Academy's League Champion, he gets taken aback by losing to you, right in front of all the students as they walk away. Unlike Blue in Kanto, who begrudgingly accepted his loss after being chewed out by Professor Oak, Kieran drops to his knees with his confidence totally shattered. Drayton even has the audacity to kick Kieran while he's down by calling him "ex-champion."
Kieran: You've got some nerve... Bringing out the ogre NOW of all times?!
Take a look at Kieran's body language right before he says that line: He covers his eyes and shakes a little. He's very likely crying, or at least, trying to force back tears.
What punctuates the sadness is just how realistic his reaction to losing is. The Pokémon franchise has such a long-standing tradition of rivals accepting their losses with dignity that Kieran's breakdown hits harder for it. For all of his jerkass behavior, it's easy to forget that Kieran is still a kid; being abandoned by all his peers and mocked for losing (especially after the journey he took just to reach this battle) is an absolute nightmare for an introvert. Not helped by the fact that it looks quite a bit like an autistic person suffering from a meltdown due to stress.
Drayton tries to soften the blow by explaining that he's worried about Kieran's fixation with surpassing the player character, but his advice falls on deaf ears. Kieran only falls further into his obsession, muttering how he'll beat you next time.
Kieran worked very hard to becomes stronger, becoming the Champion of his school, but at the cost of his own well-being and the atmosphere of the entire League Club. All of this to beat the person responsible for his change (a.k.a. you). The worst part ? It's still not enough to beat you. When he loses, Kieran seems quite afraid of the player, his confidence completely destroyed by that very same person once again, and proceeds to have a breakdown in front of his entire school. The poor kid cannot catch a break.
Kieran's Motive Rant when he tries to pull the gem that is Terapagos out of the Terastal rocks, reminding us just how inferior he feels compared to you. You look on sadly, Briar is too busy fangirling over Terapagos to notice how distressed Kieran is and Carmine tries to convince him that he's wrong and that you're not better than him. Kieran shuts Carmine down by reminding her of how quickly you managed to befriend her despite her initial hostility towards you. Carmine quickly realizes that she was, indeed, part of the problem and drove her brother to this point as much as you did.
Additionally, with Kieran being upset that he was defeated by you at his own school, he fails to understand what kind of environment he created during his time as Champion. The Elite Four comment on how different he's been acting since he returned from Kitakami and that the club isn't as fun as it used to be because of him. What was worse was that he didn't seem like he was willing to talk things out and even brushed off his sister who was very worried about him. He probably thought that his classmates respected him for his strength when they were probably afraid of him because of his behavior. In fact, if you interact with the NPCs before traveling to Area Zero, you’ll find out that his classmates are glad that he's been defeated. Imagine what that information would do to Kieran if he ever learned how they felt about him during his time as Champion.
When you beat Terapagos, Kieran is shocked that him having a Legendary Pokémon is still not enough to defeat you. It's quite sad seeing Kieran fail to understand why he keeps losing to you. It then gets worse when Briar talks him into terastalizing Terapagos into its Stellar Form; Terapagos ends up going berserk, trying to kill Kieran, destroying the Master Ball he used to catch it, and threatening to destroy Area Zero, forcing the Player and Carmine to fight it. All Kieran can do is stare in absolute horror and shock, realizing what his obsession with defeating you had caused.
Terapagos' situation also deserves some mention, as when it awakens, it immediately notices you and takes an interest in you, trying to approach you. However, Kieran, out of sheer anger and desperation, ends up completely disregarding Terapagos' feelings by quickly using a Master Ball while it's distracted, angrily screaming that Terapagos is his, and then using it against you, when it clearly had taken a liking to you. As such, it's very likely that the reason Terapagos went on a rampage, trying to kill Kieran and destroying its Master Ball isn't just because of it being terastalized and its power going out of control; it was genuinely enraged at him for what he did.
While Briar didn't have bad intentions (she only wanted to prove Heath's research correct and was too curious for her own good), she still accidentally put three teenagers in danger from her actions. She clearly feels horrible about this and apologizes to the player, Carmine, and Kieran after Terapagos has been subdued.
After you finish the story, if you go back to the Crystal Pool in Kitakami, you unlock a special cutscene — namely, Terapagos' power combined with the pool ends up temporarily bringing Professor Sada/Turo into the present.
One of the questions you ask Sada/Turo is about their family. They end up mentioning Arven, musing that he's probably at home...and that he's probably lonely. This causes them to go quiet for a moment before shaking their head and continuing their discussion with you. It's clear that, as much as they loved Arven and hated to leave him alone, their research came first.
What makes it even worse is that in the Area Zero Underdepths, you can find some notes detailing how the professor got a "white book from a child" after being transported to a "great height that smelled like sulfur" one day with no idea as to how... which turns out to be a vague recording of this very event, where you trade your Hidden Treasure of Area Zero with the professor's Scarlet/Violet Book, which means that you caused a Stable Time Loop because the Area Zero information the professor gains from your book finalizes their research into the time-machine... that will kill them and you have to stop, which leads to Briar enlisting you in helping her make the discoveries in the book. So great job, you accidentally sealed the professor's eventual doom and indirectly got Arven's parent killed. The absolute cherry on top is that from then on, the Violet/Scarlet Book returns to the table in the title screen, (having disappeared at the end of the main game), with a sunset and somber music playing, really driving home how, for better or worse, everything comes full circle.
One of the first things the Professor tells you is that they wish to finally complete their research so they can return home. It really shows that, at one time, the Professor really did want to go back and be with Arven before their obsession fully took hold.
Koraidon/Miraidon is clearly shocked but overjoyed to see their former trainer again... only to realize that the professor doesn't recognize them, resulting in confusion and suspicion (Koraidon in particular squints its eyes a few times during the entire scene in disbelief). Even then, when the professor notices that their time at the crystal pool is about to end, the Raidon is still distraught over having to watch the professor leave again, and is clearly dejected once the whole scene is over.
The craftable materials you receive from defeating wild Lapras are its teardrops. Given that Lapras was once overhunted to near extinction, the implications are... tragic, to say the least.
After you finally manage to recapture Terapagos, both Carmine and Kieran break down sobbing as they apologize to each other for the things they did to the other.
Epilogue: Mochi Mayhem
Arven spares a moment to tell us how lucky we are to have such a loving and supportive mother and later assuring Penny that her dad is overprotective because he cares about her. One can't help but think he's recalling his own issues with his parents while doing so.
Kieran watching helplessly as almost everyone in Mossui, including his sister and grandparents, are possessed by Pecharunt.
After his grandparents are taken, Kieran has a full-blown panic attack/meltdown (less severe than the last one, but still upsetting), fearfully rambling that he's going to be next and there's nothing he can do about it, even losing the shine in his eyes again. Fortunately, the player helps snap him out of it.
If you damage Arven's Mabosstiff while he's possessed by Pecharunt, Arven reacts accordingly. If you talk to him and Penny after defeating them, they'll say "Moch...iff" and "Chee... vee..." respectively, showing that even while possessed, they're genuinely saddened by their Pokemon being hurt.
A small example, but Drayton goes out of his way to keep teasingly calling Kieran "ex-Champion" for "well-earned payback", despite (or perhaps because of) the fact that it obviously upsets him.
Pecharunt's entire motivation for coming to Kitakami was to obtain Ogerpon's masks at the request of its adoptive parents. Considering the fact these events occurred long ago, it's pretty clear its parents are long dead, and that whatever Pecharunt's plans are for claiming the masks again, they are for naught.
As well, there's the old couple's ultimate fate. Without Pecharunt to keep feeding them mochi, the couple would have eventually come back to their senses and realized they'd just sent their only child on a quest for their selfish whims. And that their child would never return.
If what Kieran says is to be believed, Pecharunt's brainwashing can be broken by defeating it. It's highly possible that the couple regained their senses immediately after Ogerpon defeated Pecharunt, which just makes it even sadder.
The worst part is that its fate is all self-inflicted, as it knowingly corrupted its adoptive parents with greed-inducing mochi, because it was never satisfied by their genuine love.
It's said that Hydreigon grew ferocious because people in times long past loathed it, considering it to be evil incarnate and attacking it relentlessly.
Poor Greavard is a very loyal puppy who genuinely wants to be friends with people, but it unwittingly drains the life force of those around it, resulting in them falling unconscious or comatose, sometimes outright killing them.
Although considering how you're perfectly fine even when you have one in your team and there are several in Montenevera, it might just be another case of exaggerated Pokédex entry. Or that it's possible that those Greavard eventually figured out that this trait of theirs was the problem, and managed to get it under control to some degree.
By putting Tinkatink's dex entries together, we know that it will constantly rework its handmade hammer until satisfied with the result, but other Pokémon will often steal it. Imagine putting countless hours of work into something and having someone just rip it away from you, and suddenly Tinkaton being seen as a bully to other Pokémon makes sense.
