Delta, a reborn human girl trapped as a numbered orb, names herself and discovers her goblin minion Fran. She learns she is a Dungeon Core with a menu for building monsters, traps, and rooms using mana. The first days are a scramble for resources as she spawns goblins and mushroom spitters, defends against a farmer with a fire pistol who dies in her halls, and absorbs his fire element to unlock new construction. She discovers her dungeon has a max room limit and a boss room that turns Fran into Sir Fran, the Pig Knight, a mounted warrior. The guilt of the farmer's death weighs on her as she realizes she must make moral choices about killing to survive.

Two experienced adventurers, Ruli and Quiss, explore Delta's dungeon, appraising it as a nature-themed Mushroom Forest. They are impressed by her creativity but warn her of the world's dangers. Delta reveals her pacifist philosophy through Fran, her goblin mouthpiece, vowing not to kill. Ruli and Quiss offer advice and become her first real allies, agreeing to help her grow non-lethally. Ruli gifts her a diary that unlocks monster upgrades, and Quiss's summoned duck, Waddles, becomes a contracted Dark Drake guardian. Delta learns that people and monsters are sources of mana and DP, but she chooses to earn them through challenges and tribute rather than murder.

Delta saves enough DP to purchase a second floor, choosing a jungle theme and frog tribesman monsters. The new floor brings a massive room, a hidden mana spring, and dangerous Slimer monsters that force her first lethal defense. She discovers the challenges system, allowing adventurers to earn rewards for non-lethal feats. Hob and Gob, her contracted goblins, are attacked by a giant Black Forest Spider, and Delta evolves a Myconid to defend them. The biggest threat emerges when she digs into a circus tent containing a starving Mime ghoul named Renny. Ruli nearly kills the mime, but Delta sees a spark of trapped consciousness and offers a contract instead, saving him and adding a powerful ally to her roster of contracted monsters.

The elders of Durence, including Old Lady Jose, Haldi, and Pic, are revealed to be ancient protectors guarding a terrible secret beneath the land. Quiss and Ruli investigate the town's mysterious past, learning of a war against three dark Lords and their knights, a conflict that left the land mana-starved and the heroes bound to watch over a sealed evil. The dungeon's rising mana is reawakening the elders' old powers and memories, and Haldi sends a message to an old guild leader. Meanwhile, new villagers like the potter Japes and his curious golem Vas become entangled in the dungeon's affairs, with Vas teaching a pottery-loving mushroom and the elders cautiously monitoring Delta's growth as she digs deeper into the underground.