The game's narrative primarily consists of two timelines: the present timeline, in which the player engages with the game, and a past timeline set in the year 1500 CE. In 1500 CE, a wealthy and influential diplomat owned a large house in the Malabar region of Kerala during the Portuguese colonial era. He resided there with his wife and child, living a perilous life while maintaining delicate relationships between the Portuguese colonial administration and the native inhabitants of the region. His top priority was the safety of his family, so he kept the dangers of his work far from his home. Consequently, he was often absent from both his wife and child's lives. The diplomat's wife struggled to raise their child on her own, frequently plagued by anxiety about her husband's safety and the day-to-day challenges. Arguments were common between the diplomat and his wife, and their child, Kelan, had to endure the unhealthy tension within his family.

The game, 'Kelan's Puzzle,' depicts these family dilemmas from the perspective of the child, Kelan. These social dilemmas are encoded in the form of puzzles that the protagonist must solve to progress in the game. The game's protagonist is a distant descendant of Kelan and inherits some of his possessions as heirlooms. One day, during a move between houses, the protagonist stumbles upon Kelan's heirloom in the attic: a sealed chest. Inside, the protagonist discovers a map and a key leading to the diplomat's house. The game unfolds as the protagonist embarks on a journey to the diplomat's house, uncovering the mysterious puzzles created by Kelan centuries ago. Through solving these puzzles, the story of Kelan and the fate of his family slowly unfolds.