The central mystery reveals that the fatal glitch was caused by real-world human violence rather than computer code: while beta-testing on an uncalibrated network, Marco Han stabbed Jung Se-joo with a real knife, causing the game to link biological trauma directly to player hit points. When Marco bled to death, his avatar resurrected as an immortal, lethal NPC glitch.
Jin-woo unintentionally triggers the same phenomenon when he slays Cha Hyung-seok in an in-game duel in Granada; Hyung-seok dies of heart failure in real life and subsequently stalks Jin-woo as an undead revenant every time it rains. This glitch proves contagious to anyone forming an in-game alliance with Jin-woo, leading directly to the deaths of Secretary Seo Jung-hoon and Professor Cha Byung-jun, both of whom re-emerge as digital entities.
In the climax, Jin-woo realizes that the NPC Emma is programmed to reset the corrupted server by eliminating all glitches. Jin-woo uses the Key to Heaven to turn the phantoms of Hyung-seok, Professor Cha, and Secretary Seo into crystalline dust before offering himself up to Emma to be deleted. One year later, Se-joo has taken over J One Holdings and the game is released safely to the public; in the closing moments, rumors of an invincible cloaked player operating in the game confirm Jin-woo survived by retreating into an isolated instance dungeon.