Since The Mageseeker centers around Sylas, an Anti-Hero whose life is built on suffering, it's got plenty of heartbreaking moments.
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- The simple fact that, by this point, Demacia is so opposed to magic that despite most people worshipping her as the Veiled Lady, most of its citizenry don't even believe Morgana exists and are just clinging to any faith. The overwhelming reaction when Sylas finds her and talks to her is shock that she's even real.
- The state of the mages. Many of them have taken to living in the woods, either with Leilani's encampment or Lux's, scraping by and enduring monster attacks. That's a better fate compared to the ones in the cities; the game reveals that the scope of the Mageseekers' actions is horrific, with them abducting, executing and experimenting on an enormous number of innocent mages found within their own walls.
- Most of the rebellion have a story as to how the Mageseekers ruined their lives:
- Kara was imprisoned by them for her work, and they've perverted the teachings of her ancestor Durand into weapons against mages.
- Rukko's brother is in captivity. His father had taught the family to hide that they were mages, and Rukko's brother had always protected him. Without his brother, Rukko is alone. Even Sylas can't help but feel nothing but empathy for the boy.
- Yops was abducted and tortured by Hesbeth for years in his attempts to find the secret to her immortality. While, being a yordle, she's very upbeat, it's clear that his torments did a number on her.
- Gideon's own husband was a mage the Mageseekers drafted, and now they refuse to let him go, forcing Gideon to defect and join the rebellion.
- Aidan is separated from the woman he loves, Calliope, to protect her from the Mageseekers and to avoid getting her hurt.
- When Sylas first meets Morgana, coming to her for help, she actually refuses him, citing him as too selfish and knowing he needs to learn to be less vengeful and selfish if the mage rebellion is to succeed. Sylas ends up returning to camp despondent and enraged, not knowing what he's supposed to do if the most powerful being in Demacia has abandoned him.
- Rayn uses her abilities to torment Sylas into believing that she's the girl he killed, forcing him to fight his own nightmares and fears.
- The moment Sylas is put back into a cell he becomes desperate and enraged, exclaiming that he'll kill anyone to get out of it, even people who have come to help him. It's clear that his experiences while imprisoned have traumatized him.
- It's acknowledged that Rayn was experimented on by Hesbeth, and she even apologizes to Wisteria for her failure to kill Sylas. The poor girl's a complete victim of the Mageseekers.
- The second time Sylas and Rayn meet has a particularly sad example of Spotting the Thread. Rayn disguises herself as Lux to draw Sylas in, but Sylas figures out it's an illusion the moment "Lux" says she forgives him. Why? Because he knows that Lux will never forgive him. For just one moment, it's damn hard not to feel bad for Sylas and his self-destructive actions.
- The death of Killan. Sylas is forced to Mercy Kill his own mentor when Hesbeth takes the opportunity to mutate him into a raging monster. It's this that spurs Sylas on to finally attack Demacia's capital.
- The attack on Demacia's capital goes horrifically wrong when Sylas splits off to kill Eldred himself, forcing everyone into a position where Leilani chooses to make a Heroic Sacrifice by using a lethal spell to get them out. Sylas is literally begging her not to do it, more willing to be captured again than see her sacrifice himself for him.
- After Leilani's Heroic Sacrifice, the rebellion starts disbanding and Sylas is abandoned, standing alone as he laments feeling that he caused the death of such a good person. It's only Morgana's guidance that keeps Sylas going at all.
- The sad truth of why Morgana can't just intervene and crush the Mageseekers: She wants to, but knows that Kayle would come for Demacia if she exposed herself, forcing her back into helping from the shadows instead of letting her aid oppressed innocents. For such a heroic (if sometimes ruthless) character, it's hard to watch her acknowledge that she has the power to help but doesn't want to bring down more violence on Demacia.
- A flashback shows that, when Sylas lost control and was locked up for accidentally killing the Mageseekers, his Only Friend Wisteria almost immediately abandoned him. No wonder he was desperate for interaction when Lux arrived; he hadn't had a friend since he was a child.
- Though Garen comes to warn Lux of Wisteria's impending attack, he refuses to directly aid the mages due to fear for his own reputation and earns himself a scathing rebuke from his own sister.
- When Jarvan IV finally goes too far, Shyvana abandons him to lie in his own bed, refusing to see any more mages suffer. Jarvan is heartbroken as he realizes his own hypocrisy and how vengeance has blinded him to the point where the woman he loves most has abandoned him.
- The Final Boss fight with Wisteria has Sylas go into her memories and see what Wisteria really is: A frightened little girl who was cursed with incredibly powerful and painful magic, and was manipulated by Eldred and Hesbeth into becoming a weapon for them. Unfortunately, thanks to the way she devoted herself to the indoctrination since they were the only ones offering her relief from the pain, Wisteria is Beyond Redemption and Sylas is forced to put down his childhood friend.
- The simple fact that, despite the massive Enemy Mine between the mage rebellion, Lux's encampment, and the Demacian heroes, Sylas is still going to come for Demacia in the future. While he appreciates the change in laws he doesn't believe it'll stick and is convinced that Demacia has to fall for its mages to ever have peace. Next we see Sylas, Lux and Garen, they'll be on opposite sides in the "Warriors" short after Sylas' journey to the Freljord, which is set up at the game's end. In spite of everything that's happened between them, Sylas and Lux will never be able to be friends like they once were, with both of them lamenting the fact they'll be enemies to the end and Sylas contenting himself with the knowledge that Lux will never forgive him.
