In a time following a massive war, two girls, Chito and Yuuri, travel aimlessly through a dark abandoned factory in their Kettenkrad. After Yuuri slobbers all over her hand during her sleep, Chito realizes that they can use a wet finger to find a way out by feeling the direction of the breeze and they emerge to see a starry sky.

The next day, the girls explore a battlefield from the apocalyptic war and come across an abandoned plane. They find explosives and rations. Surprisingly, Yuuri pulls her gun on Chito and demands the last piece in a ration pack.

Taking shelter from a snowstorm, Chito and Yuuri discover a power plant with hot running water and they use it to fill a metal tank to take a makeshift bath.

Chito becomes upset at Yuuri when she throws one of Chito's books onto the fire to keep warm during the night.

The next day, after the storm passes, the girls collect drinking water in a river created by melting snow. They decide to wash their clothes as well and come across a dead fish which they roast for dinner.

While searching for the source of the fish they ate, the girls are impeded by a chasm dividing the city. They encounter another survivor named Kanazawa after he demolishes a building to create a bridge across the gap.

Kanazawa has been mapping the abandoned city and hitches a ride with the girls as they make their way using his maps. They reach the base of a tower and the group take an external freight elevator towards the upper levels of the city. However, the elevator suddenly tilts, causing Kanazawa to drop his maps and he becomes despondent. Yuuri manages to cheer him up, and in gratitude Kanazawa gives the girls his camera.

As Kanazawa sets off alone to start redrawing his maps, night falls and the girls watch the street lights come on.

Yuuri uses Kanazawa's camera to take photographs of curious tall, white stone statues around the city while Chito discovers the camera's self-timer.

Later, the girls are exploring a temple when their lantern suddenly goes out. Yuuri fumbles around in the darkness until they both discover a bright room with a pond and fake metal lily pads.

The girls explore the city and spend the night in an sparsely furnished apartment, picturing what it would be like to live in a house.

Feeling tired after staying up all night, Chito takes a midday nap and has peculiar dreams in which she is threatened by a gigantic Yuuri.

Later, the girls shelter from the rain in some ruins, taking an interest in the sound the dripping rain makes when hitting various objects.

While exploring the city, the Kettenkrad breaks down and Chito cannot fix it.

The girls encounter a woman named Ishii who offers to fix their vehicle in exchange for helping her. Together they finish constructing a simple airplane which Ishii is building from old plans in an effort to escape and reach a neighboring city.

Once completed, Ishii sets off in her airplane, only for it to fall apart shortly after take-off. Luckily, she manages to parachute out safely and she slowly drifts down to the lower levels of the city.

The girls enter a labyrinth of large pipes while following Ishii's map to a food manufacturing plant. Chito struggles with her fear of heights as she and Yuuri walk on top of the pipes before discovering there is a actually pathway inside them.

They eventually find a facility filled with machines and cooking ingredients; powdered potato, sugar and salt. The girls deduce that they were used to make rations, and using the ingredients they bake their own food bars using one of the huge ovens.

Back outdoors, the girls discover a strange place featuring tall black slabs filled with drawers. Yuuri finds a mysterious device and other seemingly meaningless objects inside them. Chito deduces that the drawers are graves containing the belongings of those who have died so they would be remembered.

Afterwards, the girls ascend a spiralling path up another tower in their Kettenkrad. They are forced to take an outside path which dangerously collapses behind them, but they manage to reach the summit.

Exploring the top of the tower, the girls find some bottles of beer and spend the night getting drunk under the moonlight.

While exploring a facility, the girls are surprised by a large construction robot which is oblivious to their presence.

They then discover an aquarium containing a single fish guarded by a robotic caretaker. It explains that the facility was once used for fish farming. The robot allows the girls to swim in one of the empty aquarium tanks, although Chito almost drowns.

Later, the large construction robot begins dismantling the facility apparently due to a bug in its programming. This leads Chito to engage the caretaker robot in a discussion about what it means to be alive. Fearing for the fish's life, the girls save it by destroying the construction robot using explosives.

The girls drive their Kettenkrad onto a goods train, finding its carriages filled with broken down machines. They disembark at the last station and ride an inclined elevator towards the top of the building.

As they ascend, Yuuri starts hearing music coming from the radio she picked up earlier which they hear more clearly as they reach the surface.

The next day, as the girls explore a large hole for some drinking water, they discover a small long, white life-form. They discover that it can communicate with them using their radio. Naming it "Nuko", the girls decide to take it with them on their journey.

Yuuri discovers that Nuko likes to eat bullets and begins feeding it while Chito finds a book on war and civilization written in English. They soon arrive at a huge clockwork-type contraption, where music starts playing on the radio again. They decide to head towards the source of the broadcast.

The girls are interrupted by an incredibly large robot which crashes down in front of them. Nuko powers up the robot and Yuuri tries out some of its weapons, causing massive destruction to the city.

The next day, the girls follow the music's signal to a still functioning submarine lying in the snow, inside of which they find an array of nuclear missiles.

While exploring the submarine, the girls inadvertently synchronize their camera to the submarine's computer and it displays their photographs, plus those Kanazawa took before giving them the camera. Among the computer files, they find videos of people and past events, including the war which led to the destruction of humanity. Later, a larger Nuko resembling the pillars they encountered earlier, suddenly appears and swallows Yuuri. Chito pursues the creature outside the submarine and finds Yuuri safe as the creature had only wanted to ingest her radio. The creature then explains that their purpose is to consume and stabilise unstable energy, like power sources and weapons. It says that life activity on Earth will eventually come to an end. It explains that their work in the city has finished as more creatures emerge from the missile tubes. It says that Yuuri and Chito are the only humans they have detected up to this level. Slowly, the tops of the creatures expand and open like mushrooms, then they begin to drift upwards together like dandelion seeds taking Nuko with them.

With the submarine now completely shut down, Chito and Yuuri continue their journey towards the top level of the city, with a new sense of camaraderie and their importance to each other.