The story continues where the last episode of the first season left off. The unconscious Lag is carried by Niche until Jiggy Pepper happens to pass by and offers them a ride back to the Bee Hive. Lag dreams of an injured Gauche waking up with amnesia. The leader of Reverse, Lawrence, who also calls himself the "One who was not Able to Become Spirit", gives him a new identity, Noir, and makes him a Marauder. After recovering, Lag reports to Largo, Aria and Dr. Thunderland Jr. on Gauche's amnesia and defection. Largo explains that Marauders steal letters from Bees working directly under Reverse, an organization intent on finding information to topple the Amberground government. Lag is instructed not to mention Gauche's defection to anyone. Niche tries to cheer Lag up but he remains despondent, wondering how he is going to explain to Sylvette about Gauche. However, Sylvette throws a "Thank You" party, with Aria's help, for Lag for finding her brother's whereabouts. Sylvette is glad Lag managed to find Gauche, and tells Lag she will await her brother's return once Lag brings him back. Lag is comforted by Sylvette's understanding and encouragement and both break down in tears. Zazie finds Niche's underpants outside Sylvette's house but she herself is nowhere to be found. Niche feels guilty on failing to protect Lag and has run away.

Lag and Connor split up in searching for Niche around town. Niche gets hungry and decides to finally eat Steak but has to cook him. She stumbles into a bakery and attempts to cook Steak, but is mistaken by the owners of the bakery for a burglar. After clearing up the misunderstanding, Niche is offered food by the owners, Jacob and Sandra Gobeni, and she reveals her problems to them. Sandra offers Niche a place to stay, but they are interrupted when a drunken street performer attempts a tightrope walk across rooftops. Lag tries to persuade him but to no avail. The rope snaps and the performer falls and Lag manages to grab him, but both are hanging dangerously from a great height. After hearing Sandra criticizing Lag's missing dingo, Niche comes to her senses and rescues Lag and the performer. Lag scolds Niche briefly and warmly and tells her to go back home with him. Jacob reveals to Lag that Gauche used to come to his maintenance shop often to repair his gun, and gives him a letter bullet. Lag will need to write a letter and roll it up inside the bullet, which he will use to fire it on Gauche to hopefully restore his memories. As Niche leaves with Lag and the others, she thanks Sandra for her bread as it made her feel happier. Sylvette welcomes Lag and Niche home.

Lag ponders over what to write in the letter bullet for Gauche, and confesses to Sylvette that he doesn't have much experience writing letters. Lag's job takes him to a mansion in the countryside where he delivers a letter to Ray Attlee. He is welcomed by a exceptionally tall maid, Kimidori. Ray wants Lag to find out who sent her picture letters of hydrangea-colored mountains, and explains the pictures remind her of her childhood while living in a village. Ray's parents received governmental positions in Central and had her moved to a location close by to receive care as she is sickly. However, she is cheered up by the letters, which she feels they tell her to keep on fighting her illness. Lag searches through town for information on the origin of the letters and finds out that the hydrangea colors came from Blue Romeo flower dyes. While searching for Niche at the mansion's garden, Lag finds Kimidori picking Blue Romeo flowers and concludes she is the sender, which she readily admits. Kimidori is glad that Ray is encouraged by her letters, but refuses to tell Lag further and makes him promise not to reveal this. However, when Lag wonders how to tell Ray, he discovers Colbasso has claimed credit for the letters for her own selfish reasons. Although Lag promised not to tell, he shoots a shindan into the letter, which reveals a flashback of Ray's childhood. It turns out Ray met and befriended Kimidori when she was young. Before she moved, Ray gives her a matching hairpin as proof of their friendship. When Kimidori grew older, her family owed debts and she is forced to sell the hairpin. Feeling guilty for having sold the hairpin, Kimidori leaves home to search for Ray's current residence and eventually finds it. She then plants the Blue Romeo in the garden to remind Ray of her childhood. Ray reunites with Kimidori and thanks her for the happy memories. Inspired, Lag decides to draw a picture for his letter to Gauche but is disappointed as his drawings are awful.

Lag is shown working on repairs for an imagery lighthouse situated in the desert. An old man addresses him as Lugh, his grandson who was born and raised in the lighthouse. Lag tells his grandfather of hearing odd voices and his grandfather dismisses them as his own imaginations. He explains to Lag that he is all that he has left and not to think of leaving the lighthouse like his parents did. While alone, Lag keeps seeing a strange four-eyed apparition telling him to leave and sees marks all over his body. Suddenly his grandfather appears and points a gun while muttering the word "hate". Lag realizes that the old man is not his grandfather and he is not his grandson. A flashback shows Zazie telling Lag about Jiggy Pepper who delivers express letters. Lag learns that Jiggy is heading to Liquid Sand River and goes to look for him there. Lag remembers who he is and realizes that the four-eyed apparition is actually Niche and Steak. While they face the old man who blames them for taking away his grandson, Jiggy confronts Gaichuu Korona who has taken over the dilapidated lighthouse. After Jiggy destroys Korona, the old man disappears and Lag and the others escape from the crumbling lighthouse. Lag remembers going to look for Jiggy and finds Gaichuu Korona instead. Upon entering the lighthouse to defeat it, he is overwhelmed and starts to halluinate himself as the old man's grandson. Lag fires a shindan into the old man's journal to find out his heart. It turns out the old man was left all alone when his son refused to become the lighthouse keeper and left with his family. He began to weave fictional tales of his grandson still living with him and becoming successor to the lighthouse. The old man eventually died and the lighthouse is left deserted. Jiggy explains that the journals the old man wrote were actually filled with hatred, and Korona consumed the heart within them which overwhelmed Lag. However, thanks to Niche, who is immune to the hallucinations, Jiggy was able to easily defeat Korona. Jiggy warns Lag not to be taken in by emotions within letters and to be strong. After paying his last respects to the old man, Lag and the others ride home with Jiggy. Jiggy tells Lag that he received a letter from Neri, his sister, and thanks him for his help.

Numerous incidents of Reverse marauders attacking Bees and stealing their letters come to a head, with Largo writing reports to the inspectors from the capital, Hazle Valentine and Caribs Garrard, who has arrived in Yuusari. Moc Sullivan comes in with news of being ambushed and losing his letters in a ravine. When Lag offers to help retrieve the letters, Hazle and Carib stop the Bees as they have no qualification to deal with Reverse, and they also suspect a leak within the Bee Hive. However, Lag, Niche and Steak stow themselves away on the inspectors' carriage. Upon discovering Lag has followed them, the inspectors decide to let him and the others follow them to the ravine. Finding the letters scattered around, Lag offers to help collect the letters when Carib tells him he will reveal what he knows about Gauche. After Lag and Niche are distracted by Carib and Hazle respectively, Carib uses a catalysing agent that resonates with the hearts in the letters to attract a gaichuu. After Lag and Niche destroy the gaichuu, Lag inadvertently finds a letter regarding the leader of Reverse, Lawrence. He reveals he is a failed man-made spirit created by an experiment sanctioned by the government and stirs up support from the populace. Gauche/Noir is confirmed to be working for Reverse. Although disappointed, Lag remains firm in delivering letters for the people. Later, Lawrence listens to the results of the experiment to attract gaichuu from the inspectors, who are revealed to be working for Reverse. Lawrence decides the time has come for Reverse to make their next move and sends Noir and Roda to the north.

Lag gets a day off from work and decides to ask Sylvette for advice on how to write the letter bullet. Lag delivers a letter to her as well, from a 10-year old girl named M. Croce. Croce likes the dolls Sylvette makes and requests to have a doll of her likeness made by tomorrow for her brother who is away. Sylvette decides to use a doll of her own likeness to rework it into Croce's image. In the morning, Sylvette goes to Dogra to deliver the doll and Lag insists on accompanying her. Sylvette wants to board a carriage but Lag warns her that letters get stolen frequently in that direction. While Lag and Sylvette sleep inside the carriage while on the way to Dogra, Autobahn, a thief disguised as an old woman steals Sylvette's package. Lag and Sylvette awaken from the commotion and try to stop Autobahn from escaping, however Lag and Autobahn fall off the carriage and the doll is thrown and left hanging over a precarious cliff. While Lag goes to retrieve the doll, Sylvette goes after Autobahn who has hijacked the carriage to make his escape. Niche arrives with Lag's gun and Lag uses it to shoot the doll back to her. The shindan resonates with the doll and reveals Gauche's thoughts before he entered Akatsuki. Sylvette decided to make a doll of her likeness to give to Gauche, but he leaves for the capital before she completes it. She wanted to help Croce as the girl's situation resembles her and Gauche's relationship. Meanwhile, Sylvette manages to stop the carriage and defeat the thief. She presents the doll to a grateful Croce upon reaching the town. Back at the Hive, Largo and Aria receive an eyewitness report of Gauche in the north.

Eyewitness reports show that Gauche/Noir and Roda were seen heading to North Yodoka, towards the town of Blue Notes Blues. Lag and Niche are sent to the town to investigate and seek out Noir. Dr. Thunderland Jr. tells them that the Maka originated from that place as well, with hopes that Niche will be able to awaken the blood of the Maka within her. While trying to keep up with Niche when nearing the outskirts of the town, Lag discovers a strange gaichuu not encountered before. Lag finds Noir's empty cartridges and attempts to fire a shindan to reveal Noir's heart, but is thrown down a crevasse and buried underneath. Meanwhile, Zazie and Wasiolka try to locate missing letters elsewhere and encounter Noir and Roda who knock them out. While trapped below the ravine, Lag watches Gauche's flashbacks and sees Lawrence asking him to join Reverse and gave a girl to assist him. Gauche had the girl take him to visit places that his former self once lived. They both watched the Bee Hive and later Sylvette from a distance. The girl shows Gauche a failed experiment from Akatsuki who is washed ashore, and explains that the government was trying to recreate ancient spirits. She reveals that she is one of the experiments that managed to live and escaped. Later, Gauche threw away his former identity and took on the name of Noir, Lawrence's personal marauder. In the present, Zazie wakes up and attacks Noir, telling him that he won't allow such a dangerous man like him to go near Lag. However, he is knocked down once again and manages to see Noir's memories of dealing with the gaichuu Lag saw earlier. Lag sees Gauche's flashback of naming the girl Roda. He realizes that Gauche still remembers his former dingo's name and so there is a chance to help him regain more memories. Niche arrives to rescue Lag and they head for the town. Niche has Lag follow her through a shortcut, telling him that she knew because she was born in Blue Notes Blues 200 years ago.

Lag reads a book on the people of Blue Notes Blues who lived peacefully with the Maka. However, this ended when people's hearts were polluted by sin. Lag discovers a cave near the lake but is told not to enter by the townspeople. They take Lag and the others back to town. When Lag asks about Noir, they confirm that Noir went to the cave, which is a path leading to Blue Notes Scale and the holy site. The mayor warns Lag not to enter as he will be punished severely. He explains the history of how the townspeople suffered when the geothermal energy around the town was stolen, leading to dead crops and widespread illness. A pregnant woman named Celica became greedy and decided to drink the water of the underground lake to gain immortality. Accompanied by Celica's return, the town returned to normal. However, Celica became quiet and eventually gave birth to twins before she died, which are the children of Maka. Lag and Niche head to Blue Notes Scale where they find frozen gaichuu and discover that Noir was there luring one outside to kill. They venture further and find the lake where another child of Maka, Niche's sister, appears. She questions Niche on her forgotten memory. The mayor and townspeople follow after Lag, where they plead the Maka for forgiveness. Niche's sister tells them that the Maka lost the ability to converse with humans and they have no interest to do so. She corrects Lag on the townspeople's story: Celica was actually forced to enter the cave to become a sacrifice for the Maka when the lack of warmth persisted, which was caused by the mining of spirit amber in the region. Celica begged the Maka to at least let her unborn child live. For the first time, the Maka sheds a tear for a human, and the tear blesses Celica. After Celica gave birth to the twins and died, the town declared them to be cursed and kept them isolated with only water as sustenance. Eventually, the town feared the existence of the twins will bring shame to them all, and the mayor's ancestor threw the children into the frozen lake.

Niche's sister attacks Lag and the townspeople but Niche defends them. Confused and angry, Niche's sister is shot by Lag with his shindan, revealing the time he first met Niche and their friendship. Despite this, Niche's sister believes Niche has forgotten how the humans treated them and attempts to kill her and Lag. Lag gets Steak to take the injured Niche to a safe place and declares that he will not let Niche's sister get away with how she hurt her own sister. Although curious at Lag having a spirit amber in his eye, Niche's sister makes another attempt to end Niche's life. However, Lag tells her that Niche is herself no matter she is human or Maka, and then fires another shindan directly at Niche's sister. A flashback shows that both sisters were always together even though they were mistreated by the townspeople, until they were separated when Niche is washed away from her sister. The sister sinks to the bottom of the lake and grows sad, eventually transforming into her adult form. Instead of searching for Niche, she decided to stay in the cave where the Maka resided as she believed that Niche would sense her heritage and make her way back like she did. Lag throws the sister back to her senses by saying she was foolish like a human as well. Her heart softened, the sister takes Niche to Tir na Lake to heal her wounds. She also explains to Lag that the gaichuu frozen in the cave are metamorphosing when they shed their last piece of heart and the Maka froze them to prevent them from causing chaos to the world. The sister then entrusts Niche to Lag to help her mature, though Niche stays in the lake to heal her wounds for the time being. As Lag leaves, both the Maka and Niche's sister sense him as the Light, looking forward to what he will become.

Zazie wakes up with Lag beside him. He learns that Lag came to the city of Pierce when he heard that a Bee was wounded and taken here. From what both Zazie's eyewitness accounts of a molting gaichuu and what Niche's sister told him, Lag learns that the spirit insects were chosen creatures born from the fusion of small insects and spirit energy beings in the land. But when their last bit of heart has shed away, they turn into gaichuu. It seems that the spirit insects encased in amber given to Bees pose no threat, but the ones without will threaten world order and bring peril to the land. Lag becomes concerned about what the government does in this country and how it came to be. Lag and Zazie head off for the town of Lament by carriage and meet Connor there, who is making his deliveries. Connor tells them that he has fallen in love with a girl from the Veritably Abbey who sold cookies to him for one time, unbeknownst to them, is actually Roda. Connor buys cookies from a red-headed girl named Sunny who tells them that the white-haired girl only came to the Abbey once. After seeing Roda nearby, Lag comes to the conclusion that the Abbey is a base for Reverse. He tells Connor to head back to the Hive and alert Largo to this place while he disguises as a girl to gain access to the Abbey, as men are not allowed on the premises. After Sunny invites Lag in for shelter, she heads for her prayers. Lag follows and discovers that the nuns are led by Roda to believe that by sacrificing themselves, they will help revolutionize the government and save their fellow humans. Lag goes off to explore but is caught by Roda, who recognizes him, which leads to a short fight. Roda tells Lag they will exact ultimate revenge on the government, using the molten gaichuu as a weapon.

While the nuns head for the prayer hill of Angel Wings to prepare for their sacrifice, Sunny is ordered to poison Connor with her cookies. Connor goes into the abbey to investigate the claims of Reverse using it as a base, and encounters Lag and Roda fighting. Roda takes Connor hostage and makes her escape, leaving Connor confused and disappointed that she is a member of Reverse all along. Hazle and Caribs, the inspectors from Akatsuki, return and destroy the abbey with explosives to conceal Reverse's activities while making a fake report back to the government. After Lag and Connor make it out of the debris safely, Lag goes after Roda. Sunny finds Connor and gives him the cookies to eat, which causes him to collapse. Sunny and the abbey's sad past is revealed: despite trying to work hard, the abbey never rose above poverty and hardship, which made them easy prey for Reverse to convince them of its ideals. Before leaving for Angel Wings, Sunny leaves a note for Connor, who is only paralyzed by a special medicine instead of the poison. Lag tries to convince Roda what Reverse does is wrong, but Roda attacks him anyway, leading to Zazie coming to Lag's rescue. The molten gaichuu Cabernet arrives, and Lag figures out that Reverse wants the abbey nuns to become sacrifices for Cabernet to drain their hearts. Noir appears and attacks, but Lag realizes he lost his letter bullet to Roda. With Zazie distracting Noir, Lag pours his heart into his shindan and fires at Noir, hitting him. Connor goes after Sunny, who stated in her note that she isn't sure whether being a sacrifice is right, but she wanted everyone to be happy, including Connor whom she liked. Connor arrives too late to save Sunny, as her and the nuns' hearts are taken by Cabernet. After being hit by Lag's shindan, Gauche appears to recognize Lag.

Gauche appears to have recovered to his former self, but he walks away from Lag. Lag goes after him but is blocked by Roda. A large group of gaichuu, Lao-Lao, arrives to attack them. Lag and Zazie's attacks are not able to fend off Lao-Lao. Unknown to them, the traitorous capital inspectors are controlling the gaichuu to attack them while Cabernet gets away. However Niche arrives on the scene to restrain Lao-Lao with a new ability using her hair, and Lag destroys the gaichuu in one shot. Roda tries to follow Noir but she falls through a crevasse but Lag grabs her in the nick of time. Roda does not understand why he would save her and Lag explains that he feels Roda is the same Roda that was Gauche's former dingo, and encourages her to keep fighting to protect her master. However, Roda frees herself of Lag's grip and seemingly falls to her death, lamenting that she is Reverse's Roda. However, she leaves Lag the letter bullet she stole from him. While Zazie fends off Cabernet, Lag goes after Noir to attempt reviving his memories of being Gauche. When Connor arrives with a comatose Sunny, Lag becomes disappointed with what Reverse and Noir have done. Spurred by his emotions, Lag's spirit amber charges up. Noir fires a shindan at him but Lag easily erases it. Lag declares that he will erase him from existance and shoots Noir, knocking him out. Cabernet is attracted to the heart Lag radiates and grabs both him and Noir. Lag is initially uable to target Cabernet's weak point, but Noir awakes and directs him to attack together. Cabernet is hit by both shindans but gets away. In the aftermath, Lag is told Connor will stay with Sunny until she wakes while Zazie goes after Cabernet. Lag brings a comatose Noir back to the Bee Hive where Thunderland Jr. will analyse his condition. Aria and Sylvette are glad that Lag has brought back Gauche, and Lag feels that for a brief moment Gauche came back to him when they both attacked Cabernet.

On the government's request, Largo sends Zazie in charge of the personnel that will head east to destroy Cabernet. Lag undergoes examination by Dr. Thunderland Jr. after he fired too many shindans. Aria is sent to deliver a letter to Houdai Franklin, a man who worked aboard the airship. Hearing this, Lag sends a reluctant Niche to accompany Aria as her temporary dingo. The duo head for Black Cherry Pond which will lead to Houdai's current residence, which is rife with gaichuu. While crossing the pond, they are attacked by gaichuu Tequila Sunrise. Despite Aria's objections, Niche goes to attack the gaichuu, prompting Aria to use her shingengakki to attack. However she loses concentration as she hasn't attacked for a long time. When the gaichuu captures Aria, Niche sees her memories of the time she grew up and later worked with her dingo, a dog named Bolt. Thanks to Bolt, she plotted a set of safe delivery routes for the rest of the bees. Despite being disappointed she has no worthy skill to deliver letters, Aria continues to rely on Bolt for his support. Niche frees Aria from the gaichuu and encourages her to fight, saying she's the only one to defeat them and translated Bolt's howls that he will always protect her. Aria is encouraged and finally gains the concentration to destroy Tequila Sunrise. A flashback shows Aria worried about Gauche's safety and well-being, while Bolt has to retire from his duties due to old age. Aria wanted to quit but is told by Largo to stay on as administrative assistant. Meanwhile Lawrence talks to Signal, he gatekeeper of the bridge to Bifrost, who is revealed to be supporting Reverse with his brother. Lawrence informs Signal that Cabernet has been spotted and his people will soon direct it to attack Akatsuki.

Aria and Niche head to Houdai Franklin's house. Franklin attacks them upon meeting but Aria manages to convince him that she just wants to know the truth about the Day of Flicker. In flashback, Franklin was an engineer working on the airship with his friend Negich. The purpose of using the airship to travel to the artificial sun wasn't explained to the construction crew. A number of characters such as Dr. Thunderland Jr., a group of Bee triplets (with two of them serving as the gatekeeper between Bifrost and Yuusari in the present) were present aboard the ship. When Franklin wanted to steer the ship in order to get a clearer look at Akatsuki, the artificial sun gave out and flickered a few times. This momentary lapse in the sun's rays caused a huge disturbance among the crew, Franklin included, who claimed to see a monster in the sun calling for its "mother". Soon after, the airship crashed and most of them died except for Franklin, Thunderland Jr., the triplets and Balor, the general commander sent to oversee the operation. Each of them are left either partially or completely blinded. Meanwhile, Lag takes a turn for the worse and his heart energies are in danger of overflowing. When Thunderland Jr. and his staff try to stop the flow, they witness Lag involuntarily summoning visual flashbacks of his life with some imagery appearing not to be seen elsewhere before. After Lag recovers, Gauche wakes up with his memories returned, much to the delight of everyone, especially Sylvette. While Lag reunites with Gauche, Franklin tells Aria that he believes that the artificial sun is an abomination that will eventually consume all the hearts of the inhabitants and it is too late for Gauche to ever recover his lost memories.

Lag requests Largo and Thunderland Jr. to allow Gauche to go back home with Sylvette, but the request is denied. Both men want to know how Gauche is able to regain his lost heart as well as what happened during the period he was in Akatsuki. However, Largo allows Gauche to return home for the night as he believes this will be better for his well-being. Lag tells Gauche the good news and will pick him up after his delivery, but Gauche decides to accompany him as his dingo. Although Lag feels that he's not a wonderful Bee, Gauche tells him that by returning his lost heart to him, he is one. Gauche apologizes to Lag for not able to keep his promise to look for his mother in Akatsuki. Back home, Sylvette welcomes Gauche back and thanks Lag for keeping his promise. Roda returns alive, as she spies on Gauche at his house. Thunderland Jr. warns Largo that since Gauche can access the memories that Lag does, it's possible he's still Noir pulling off a deception on them. The next morning, Lag discovers that Gauche has disappeared from his room. Meanwhile, the capital inspectors inform Lawrence on Gauche's regaining his memories. Since he can't be a Marauder anymore, Lawrence orders the inspectors to dispose of him. He then peers down a cliff to an unknown gaichuu.

Sylvette goes into town looking for her brother, while Lag goes to the Bee Hive. He finds Dr. Thunderland Jr. and Hunt, who has become his assistant, but both of them have not seen Gauche returning. A flashback shows that after Roda survived her fall, she made her way to Yuusari to look for Noir. Hunt and Sarah rescue her from some thugs and they give her a place to stay. She learns from them that Gauche has woken up in the Bee Hive. Roda follows Lag and Gauche around but is eventually found by Sarah, who takes her under her wing in the employment agency when she learns that Roda was a dingo. Largo orders the Bees for a city wide search and Lag stumbles onto Sarah's agency. He tells Sarah that Gauche has disappeared and Roda immediately leaves the building, but is sensed by Niche. After reporting the failure in the search, Niche decides to head out and search for Gauche herself but encounters Roda. Both fight, however Niche is much stronger and nearly overpowers Roda until Gauche steps in to save her. Over Niche's protests, Gauche declares himself as Noir and leaves with Roda. Lag arrives too late to learn from Niche the bad news.