- Both endings have their downsides. Choosing to put the lightbulb in the spire will give the world light once more, but it'll end up dying anyway and Niko will be trapped forever, miserable, and unable to return home. Choose to smash the lightbulb and Niko will return home, but the world will be left in darkness for the rest of its life, and the residents will never see the sun again.
- In the updated rerelease there's the scene at the café where Niko reminisces about their mother and bursts into tears because of how much they miss her. It's a powerful reminder of the fact that Niko, despite being a chosen saviour and having a literal god guiding them, is just a child who was suddenly thrust into a completely foreign world and burdened with a massive responsibility while having no say in the matter.
- The fate of several NPCs in the Solstice run. Silver is caught by the squares while she's trying to get out of the mines with Niko and Prototype. Calamus and Alula are left stranded at the graveyard by squares, and Cedric says he'll come back for them, but his plane is glitched out too. They're basically left waiting for help that will never come while the squares engulf the whole island. Finally, Lamplighter travels with Niko in an elevator, but the squares cut the door off before he can get out. He's left trapped as he waits for the squares to get him...
- Heck, the reaction Niko has when they find out that they've already gone through all of this before is enough to merit its own example. Knowing that you've done this before and that your choice didn't matter, not to mention the world that choice hinged on isn't "real" either, is bad enough. But on top of that, all Niko can think is that you, the "god of this world", must be cruel to continue this cycle. The player has no chance to explain the situation to Niko, and while Prototype does his best to explain in the player's place, the fallout of Niko's reaction leads to the increased rate of the world's decay. Things get better and Niko does eventually realize you're trying to do what's best for both them and the world, but it's still a significant Player Punch to go through.
Tear Jerker / OneShot