The Binding of Isaac: Rebirth's storyline is based off the eponymous Bible story. Isaac (a kid) and his mother live in a small home situated on a hill, both peacefully keeping to themselves, with Isaac drawing doodles and playing with his toys while his mother watches Christian broadcasts on the television. Isaac's mother then hears "a voice from above", stating her son is corrupted with sin and must be saved. It asks her to remove all sin from Isaac to save him. She obliges, taking away his toys, pictures, his handheld video game console and even the clothes on his back.
The voice again calls out to Isaac's mother, stating Isaac must be isolated from all the evil in the world. Once again, she follows its command and locks Isaac in his room. Finally, the voice speaks to her again. It states she has done well but says it still questions her faith and commands she must sacrifice Isaac. She obliges, grabbing a kitchen knife and goes to Isaac's room. Isaac is watching through a sizable crack in his door and starts to panic. He finds a trapdoor under the rug, and just as his mother bursts in, he opens the trapdoor and jumps down it. The game then transitions to the title screen.
Shown throughout the game at loading points between floors is Isaac recollecting about his childhood while curled up in a fetal position and crying. These purportedly show parts of his life, showing Isaac had a difficult childhood ranging from rejection from his mother to bullying from his classmates. However, some images show impossible scenes that cannot have happened but are rather Isaac's own fears. Along with that, the game resumes with Isaac waking up on the next floor making it possible that the memories are merely made up dreams.
The game has an epiloge and 16 ending scenes, making the storyline distorted and non-linear as the game continues
This game contains....