On the outskirts of the country of Helvetia rests the tranquil town of Seize. Upon its cobbled streets, citizens go about their daily lives, undisturbed by the increasingly tense military relations between Helvetia and the neighboring Roman Empire.
It is under these circumstances that the 1121st platoon of the Helvetian army, stationed at the Clocktower Fortress in Seize, receives a new recruit in the young and spirited Kanata Sorami. Having joined the military to fulfill her dream of learning to play the bugle, she excitedly accepts the tutelage of the Sergeant Major, Rio Kazumiya, who happens to be a skilled trumpeter. Working alongside them are the aloof mechanic, Noël Kannagi, the feisty gunner, Kureha Suminoya, and the compassionate Captain Felicia Heideman; together, they experience the beauty of life in Seize and the lasting joy of a community that has persevered in spite of the crumbling world around them.
A young girl named Kanata Sorami joins the army with the hope of learning to become a good bugler. She is assigned to a place called Seize, which is currently holding a festival where people splash each other with water. She is found by her superior, Rio Kazumiya, who gives her a bath and tells her about the legend of the Fire Maiden. While looking at a bell owned by Rio’s father, an owl steals it, forcing Rio to stop Kanata falling off the balcony trying to get it. As Rio participates in the festival, Kanata decides to search for the bell. She finds it hanging off a ledge, but when she goes to get it she falls into the lake, where she sees the golden skeleton of a winged creature. Stranded at the bottom of a canyon, she plays her bugle where she is responded to by Rio on her trumpet. She takes her to the Time Telling Fortress and plays the trumpet as the sun rises, introducing herself as Kanata’s bugling teacher.
During breakfast, Kanata is introduced to the other members of the 1121st Platoon; Felicia Heideman, Noel Kannagi and Kureha Suminoya. Kureha shows some hostility towards Kanata, but she is assigned to show her around the fort. When Kureha takes Kanata to see the tank of the squadron is kept, which is in the process of being repaired, Kureha expresses her depression because the military often ignores the squadron’s existence. Later that night, Noel and Kanata claim they saw a ghost in the barracks, so Kanata and Kureha are sent to investigate. They learn the place used to be a school. Kureha laments that their platoon is in the middle of nowhere and is generally ignored. The two are surprised by an owl, the same one that stole Rio’s bell, but with Kureha’s help they manage to capture it. They decide to keep it and name it Shuko.
As the others go to pick up some supplies, Kanata spends the afternoon training with Rio. Just then, Kanata comes down with a fever, reminding Rio of when her mother fell ill. Out of medicine, Rio gets help from a priestess named Yumina, who diagnoses her with malaria and treats her. When Kanata wakes up, she explains she was overworking herself since she felt useless. She also mentions to Rio that she always wanted to play "Amazing Grace," having heard from a bugler she met when she was little. Rio then plays Amazing Grace from one of the tanks, explaining that a squad, much like a song, is composed of many different parts.
Kanata goes with Noel to get more parts for their tank, the Takemikazuchi. They visit a glassworks shop run by Naomi, the lady who helped Kanata when she first arrived, and she takes interest in a glass dolphin. Later on, they run into Yumina and a couple of kids. The boy, Seiya, gets angry at them, since he hates soldiers due to the death of his parents. Kanata and Noel then go to a glassworks factory, where they are having trouble replicating the optical lens needed for the tank. Having noticed Noel feel down following the argument with Seiya, Kanata tells her it’s not the machine that’s good or bad, but the person inside it. After speaking with the workers, Carl and Maria, they give Kanata advice that allows her to become better at playing the bugle. This in turns helps Noel determine the effective lens samples by having Kanata check their sound. The tank works and Noel smiles for the first time in a while.
The squad take a "field trip" to the mountains where some observers need a maintenance check. Kanata, Kureha and Noël are forced to carry heavy backpacks on their hike up. Whilst they find the first observer quickly, the next one lies at the top of a mountain. They take a break at a running river but soon return to find their backsacks ravaged of their food and their compass. Despite the hunger, they eventually manage to find the remaining observers. At the last observer, Filicia shows the others signatures left by former members who had observed No Man’s Land from that point. They are then taken to a hot spring where Rio, who had fought against a boar to get some berries, awaits.
The group give Kanata her paycheck early and she goes into town to spend it. In actuality, it is to get her out of the way whilst the others illegally trade some calvados to make some money. When they get word from Naomi that some investigators are planning to snoop in on the deal, they stage a mock shoot out to scare them off. Meanwhile, one of Yumina’s orphans, Mishio, runs off when she objects to having her hair brushed. Kanata finds her at the market, where she reveals she is looking for a certain box. Yumina explains to Kanata the box was a memento of Mishio’s mother that was taken when she died. Mishio ends up on a roof, but the noise from the mock shoot out causes her to slip. Kanata manages to save her before she falls, though it causes some rocks to fall that smash into the investigators’ car. While apologizing to Naomi, they notice the box Mishio had been looking for. Mishio decides to give it to Yumina as a symbol of how much she cares for her.
Everyone prepares for Fiesta des Lumiéres, which starts to bring bad memories for Filicia, whose comrades were killed in a fierce battle. While wandering in the battlefield with a heavily wounded arm, she falls into a tunnel which was well buried under the ruin of the past civilization, where she finds a corpse of a soldier of the old era. In her illusion, the corpse approaches her, apologise for the war they could not win, which makes life vanish from the sea, while on the ground humanity is falling apart. Then Filicia was rescued by someone named Princess Iliya. The girls later send off paper lanterns in the river and Filicia tells Rio her reason for living. Meanwhile, a priest seems to recognize Rio from somewhere.
The squad are asked to watch over the emergency phone and wait for a call to check it is still in order, so Kanata decides to take responsibility whilst the others go out for various tasks. Before Rio leaves, she gives Kanata a trumpet book, signed by an Iliya Arkadia. Later, Seiya, Mishio and the Priest arrive, and decide to help Kanata practise using a phone, but a mess is made when Mishio spooks Shuko. Yumina arrives at that point, scolds the others and gives Kanata a change of clothes. Afterwards, Kanata needs the toilet but can’t leave her post, so she holds out until Rio comes back. The phone then rings and Rio answers, hearing a voice she’s not too fond of asking her to save Helvetia.
Kanata and the others wonder if something is strange about Rio’s behaviour. As a typhoon settles in, Claus arrives with a package for Rio. After the others tell Kanata about Princess Iliya, they hear from Yumina that Seiya has gone missing and go into the city to search for him. Kureha and Claus find Mishio, who leads them to Seiya, who was trying to protect some eggplants. Whilst they manage to get Seiya to safety, Kureha and Claus are blocked off by a rockfall. It is revealed that Claus isn’t actually the infamous Desert Wolf that Kureha believed him to be. As the others send a wire over, the ground collapses beneath them, but Claus manages to rescue Kureha before she falls in. Despite knowing he is a fake, she still recognises Claus as the person she admires.
Kanata asks Kureha to tell her more about Princess Iliya. Yumina asks Kanata and Rio to check up on an old woman named Jacott who lives in the mountains. The two later take a walk where Rio talks to Kanata about her half-sister. As the snow falls, Yacott, filled with memories about her love, runs off into the snow and never returns. Rio reveals she is the half-sister of Iliya, and decides to leave the fortress to help improve relations between the warring sides, leaving Kanata her trumpet.
Whilst on patrol in the snow, Kanata and Kureha stumble upon an unconscious Roman soldier. Noël seems to recognize her and asks to look over her. She wakes up the next day and introduces herself as Aisha Aldola, though she is unable to speak Helvetian. Kanata and Noël spend some time with her, and Kanata is surprised she knows how to play Amazing Grace. Later, Naomi and Yumina arrive, informing them that Helvetian armies are heading towards the fortress. Yumina acts as a translator for Aisha, who says that she wants to see the Angel Fossil (the one Kanata saw underwater in the first episode), the remains of the "Angel of the Apocalypse" that brought upon judgment to the world of the distant past.
Confronted by soldiers from the 9th Division, Aisha suffers serious injury in front of a frightened Noël. Meanwhile, Filicia takes Col. Hopkins hostage and orders his forces to leave the fortress as they barricade themselves inside. Col. Hopkins divulges his intention to use Aisha to instigate war, in addition to revealing his connection with Noël who once worked with him in reconstructing an ancient bioweapons technology that resulted in the deaths of many people. After being locked up in the distillery, he manages to make his escape in secret. While on tower patrol, Kanata hears a faint and distant signal for cease-fire prompting her to tell the others. Naomi with the support of the townspeople try to convince the 9th Division of the signal for cease-fire but are arrested by Col. Hopkins. Out of options and with an injured Aisha in tow, the girls decide to use the restored Takemikazuchi to stop the 9th Division and prevent all-out war between the nations.