Throughout the film, the origin of Cheol-soo is quietly hinted to be a dark military experiment conducted during or after the Korean War by a disgraced scientist whose former home the family now occupies. When Ji-tae beats Cheol-soo and frames him for viciousness, Cheol-soo's genetic mutations trigger a full physical metamorphosis into a monstrous beast to shield Sun-yi, exposing him to lethal retaliation from the police and military.
To prevent Cheol-soo from being executed, Sun-yi makes the agonizing decision to reject him forcibly, slapping him and throwing rocks while crying, forcing him to run into the mountains. Before departing the village forever, she leaves a note in the barn: "Wait for me, I'll come back." Sun-yi subsequently moves to America, marries, raises children, and lives a conventional life, never returning to the estate.
Forty-seven years later, the elderly Sun-yi returns to inspect the house before its sale and enters the preserved shed at night. In a devastating reveal, she finds Cheol-soo waiting in the pristine room, having not aged a single day. He hands her the repaired guitar and reads aloud the storybook she once taught him. Overcome with grief and guilt, Sun-yi confesses she lived a selfish, ordinary life, but Cheol-soo comforts her, stating she is still beautiful. The hidden tragedy is that despite their spiritual reunion, Sun-yi leaves the next morning with her granddaughter, choosing to cancel the sale so Cheol-soo's haven remains protected, while Cheol-soo watches her depart alone, destined to spend eternity in solitary remembrance.