The scene I've chosen is from Conker's Bad Fur Day; it's a game that I played years ago, and which started off with an irreverent South Park-type plot. Towards the end, I noticed that it started becoming darker, and more violent, and it really started to hit home in the penultimate chapter, "War". This scene is just before the final boss, in "Heist", and SPOILERS:
Conker's girlfriend, Berri, is set up as a main character, despite not appearing that much until the final chapter. Just before the final boss though, she is killed (the Panther King also dies in this scene); the other moment that I considered using was the final moments from this game, when - after exploiting the game's locking to save himself, and become king, Conker realised that he forgot to stop Berri's untimely death.