* Melia's final Heart to Heart, [[spoiler: in which she gives up pursuing Shulk.]]
* In the Battle for Colony 9, Fiora tries to pull a BigDamnHeroes to save the party from Metal Face... [[spoiler:only to get impaled. [[RoaringRampageOfRevenge Shulk's reaction is perfectly justified.]]]]
** To make matters worse, in his later appearances in the game, Metal Face just ''loves'' to rub in the fact that yes, [[spoiler:he killed Fiora. Yes, he enjoyed doing it. No, there isn't ''anything'' you can do to bring her back. Every time that bastard shows up, you just wanna shove the Monado up his ass, ''but you can't.'' ''[[KungFuProofMook He's immune to it]]''. You can't even TRY to avenge her because of that!]]
*** Let's face it, Metal Face is a walking BerserkButton for Shulk and co. The worst part? ''He knows that and loves every second of it''.
* The WhamEpisode on Prison Island. To sum up [[spoiler: the party utterly fails to prevent Emperor Sorean's death at Metal Face's claws, barely makes it in time to receive the Monado upgrade from Zanza before Metal Face kills him, too, and when it finally comes time to pay Metal Face back for all the death and destruction he's caused, he doesn't even take the brunt of the new Monado's wrath. Who does, you ask? None other than Fiora, revealed to be Face Nemesis' pilot when she takes a slash to the chest from Shulk. This sets off a HeroicBSOD from most of the party, as much of Shulk's reason for fighting the mechon was to avenge Fiora's death at the beginning of the game, only for her to turn up alive and on Mechonis' side. And the soundtrack at the end? The Main Theme, which is an orchestral remix of Shulk and Fiora's leitmotif, just to twist the knife even further.]]
* [[spoiler:A testament to the voice acting in the English version: The sheer [[EtTuBrute heartbreak]] in Egil's voice when he realizes even his own goddess has turned against him.]]
* The look of betrayal on Shulk's face as he realizes that [[spoiler: Dickson- the man who basically raised him- has just literally shot him in the back.]]
* [[spoiler: Melia watching her people, including her brother get mutated into Telethia. That particular plot point gets even worse when you look at your Relationship chart....]]
** Even worse, several quests after that event have you going back and [[spoiler:delivering a MercyKill to many of the transformed Telethia. The "Released from Duty" quest is especially heartbreaking]].
** The quest "I Will Always Remember You" is equally heartbreaking, especially since it follows a chain quest where you reunited two childhood friends. The quest giver in question ask you to [[spoiler: not only kill her friend, but also her friend's mother who despite being turned into Telethia protected her and allowed her to escape]].
** The quest "A Memento from Daddy" available after Mechonis Core, is a sneaky punch to the gut. [[spoiler:It involves the two mischievous, but now orphaned High Entia children. The sister Cian doesn't understand what happened to her dad and misses him dearly, so her brother Atael asks you to find something their father buried back in Alcamoth to cheer her up. It turns out to be a family photo, and that isn't too hard to obtain if the party can handle the Telethia swarming Alcamoth. However, there's a hidden objective once you pick up the memento: the party encounters ''"Telethia Vol'Aran", Atael and Cian's father as a Telethia'', who they must kill to properly fulfill the quest. A tragic way to think of it is that since the party would know how much Vol'Aren loved his children (the affinity even says as such), they decided to secretly put these children's father to rest for them.]]
* Good news: [[spoiler:Fiora's back in your party as the final member! Bad news after [[WhamEpisode Mechonis Core]]: Meyneth's death deprives her of the chest component - Meyneth's Monado - that kept her functioning. Now that she's running on small reserve energy, she doesn't have much longer before she's just going to stop working. ''And she knows it.'' It's admirable to know that she makes the decision to keep on fighting while knowing this, but that doesn't make her impending fate any less heartbreaking.]]
* Xord. In the main story, he's nothing but a [[SmugSnake Smug]] [[TheBrute Brute]] you take great joy in beating the crap out of. But if you've been taking care to speak to your [=NPCs=], you'll realize that [[spoiler: he was Desiree's father.]]
* [[spoiler: Dickson's death. Yeah, the guy was a JerkAss who literally shot Shulk InTheBack, but he was also Dunban's war buddy and one of Shulk's father figures, and there were a few moments where it looked like he might have genuinely had a soft spot for the Colony 9 kids. When Fiora tells Shulk that Dickson's wounds are too severe to survive, the camera stops for a moment on Shulk's face, as if he's shedding a tear as the party heads onward to confront Zanza.]]
-->[[spoiler:"Looks like the student... has finally surpassed the teacher."]]
* Lunara, the little High Entia Girl that stays at the entrance of Alcamoth every night waiting for her dad to come home.
* Seeing the [[spoiler: once tall Mechonis in ruins after Zanza mercilessly destroys it. The sky never looks the same. On top of that, Egil fought to his last breath fighting Zanza and saving the party. He also indirectly gives you the opening needed to defeat Zanza. Despite all Egil did, you can't help shed tears for the guy as he goes down with the ship]].