Little Nightmares stars a young boy with a bag on his head named Mono. Throughout the game, Mono is drawn to television sets that display a transmission of a long hallway that ends at a door with an eyeball symbol. He is able to enter the TVs as if they were portals, but he can never quite reach the door before he's sucked back out to the real world. This will be very important later on.
He starts his adventure by traveling through a trap-infested forest before arriving at a creepy old house. Inside, he finds rotting meat and mannequins that are most likely the taxidermied remains of unlucky humans. He also finds a little girl playing with a music box who is being held hostage in the basement. He frees the girl by smashing the door with an ax, but instead of thanking him, she scurries away as fast as she can.
Mono finds the girl upstairs and the two begin working together in order to survive. They eventually discover the owner of the house who is a violent Hunter wearing a sack over his head. Upon seeing the children trying to escape, he chases after them with a shotgun. The two break into a small shed where a spare shotgun is being stored and shoot The Hunter, which presumably kills him. They find a large, discarded door and use it as a raft to cross a body of water. This takes them to the shores of a place known as The Pale City.
The two enter a school that is surprisingly populated with children. Of course, they're not normal children since this is Little Nightmares. They're actually strange living dolls with porcelain heads known as Bullies. They're all being taught by a woman called The Teacher, who has the bizarre ability to stretch out her neck to absurd lengths like Elastic Man. After the girl is captured by the Bullies, Mono rescues her again and the two barely escape from the school. They walk out into the streets during a heavy rainstorm. It is here that the little girl finds a familiar yellow raincoat and puts it on. So yeah, she's Six from the first game. What a twist!
Mono and Six make it through a dark hospital filled with living mannequins who can only be stopped by light. The two end up in the lower levels where they encounter a huge man called The Doctor. He's a grotesquely bulbous figure who scampers across the ceiling like some sort of spider. After a tense chase, Mono manages to trick The Doctor into entering an incinerator and burns him alive.
At this point, the two have seen a giant spire that's far off in the distance of the city. This is the Signal Tower and it's broadcasting a transmission that warps the bodies and minds of those who watch it. It explains the strange mutations that the characters we've come across have. It also explains the appearance of the hypnotized citizens known as The Viewers, whose faces have been turned into featureless, sunken flesh folds.
Mono has been lured to various TV sets a few times and almost reached the end of the hallway before being pulled away by Six. Mono finally enters one of the TVs and makes it to the end of the hallway. He opens the door with the eyeball on it, which turns out to be a big mistake. This unleashes a ghostly entity known as The Thin Man, who begins to hunt down the children upon his release. While Mono manages to hide from him, Six isn't as lucky and is sucked into the TV. The Thin Man continues to chase Mono until he's finally cornered in the middle of the city. It is here that we find out that Mono possesses similar powers to that of The Thin Man. He is able to use the transmission to defeat The Thin Man, which causes him to vanish. He then enters the Signal Tower to rescue Six once again.
Inside the Signal Tower is a strange, pinkish-purple alternate dimension where gravity and time seem to be distorted. After some searching, Mono finds Six. The only problem is that the Signal Tower has transformed her into a giant, twisted version of herself. This Six is obsessed with a music box that's similar to the one she was playing with when Mono originally saved her. Seeing that this music box is the object behind her transformation, Mono destroys it. Six tries to stop him, but he succeeds and frees her from the influence of the transmission.
The Signal Tower then suddenly begins to fall apart revealing that underneath the building is an overwhelming mass of gooey flesh and eyeballs. The two children run away as a wave of flesh tries to crush them. As a bridge towards the exit begins to crumble, Mono leaps towards a ledge, and Six manages to catch him. However, while she could easily lift him up, Six decides to let him go and Mono falls to the depths of the Signal Tower as Six nonchalantly escapes. She's not a very good friend
Mono now finds himself stranded at the bottom of the tower. As he walks among the pulsating flesh and eyeballs, he comes across a single wooden chair. He sits down and he suddenly seems to be in a normal-looking room. We then watch a montage of him aging. He grows taller and thinner. He has become The Thin Man.
In the secret ending, we see Six exit through a TV set. As she stands, a glitched, shadow version of herself appears and looks down toward a drawing of the massive ship from the first game, The Maw. We then hear the familiar rumbling of Six's stomach. The events of this game were a prequel to the original Little Nightmares, as it shows the origins of Six's selfish survivalism, her impetus to reach The Maw, and the birth of her constant hunger.