Niche thinks she has failed at being Lag's dingo, so she runs away from home with her pet(?) Steak. Worried, Lag and Connor head out to search for Niche. However Niche, hungry and wandering aimlessly around town, sneaks into the bread and weapons shop Sinners and tries to finally cook Steak, but the Gobenis catch her in the act.

One day, while on a delivery to a certain mansion, Lag is asked by Ray Attlee the owner of the mansion, to search for the person who sent a picture-letter to her. Ray says that the pictures in the letters reminded her of her hometown, and gave her the will to continue to live on and fight her illness. Lag, after being called a "Letter Specialist" by Ray, decides not to rely on his shindan that allows him to see the heart contained in letters, and does his best to search for the sender. He discovers that the paints used to paint the letters have some connection to Ray's hometown, and then...

"Get away from here"... The boy Lugh works together with an old man he calls "Grandpa" in an imagery lighthouse built out in the wilderness, but he keeps hearing voices from somewhere. Around the same time, Jiggy Pepper is passing by the area on a delivery, and notices that a Gaichuu, Korona, has made a nest on top of the imagery lighthouse. Riding his "iron horse" up the imagery lighthouse, Jiggy Pepper's shindan Lapis Lazuli explodes!

Two inspectors from the capital, Akatsuki, come to the Bee Hive. Caribs Garrard and his dingo, Hazle Valentine. They came to investigate a string of letter robberies happening to the south. During one of them, Moc Sullivan is attacked, and the letters he was carrying fall into a ravine. Garrard suspects that there's someone on the inside for Reverse, since they know so much about the Letter Bee's routes and movements, so he forbids them from going to the south. However, one of the letters Moc was carrying was a letter from a sick girl that Lag dictated for her...

Sylvette receives a fan letter addressed to her from a girl named M. Croce, asking her to make a doll that looks like her to give to her brother who will be leaving his hometown to work in a coal mine shortly. The doll maker, Sylvette, hurries to make the doll, and after spending all night, heads out the next morning to deliver it. Lag is worried and goes with her, but the two of them are tired and end up falling asleep on the rhino carriage!

A person spotted Noir up in the northern reaches of Yodaka. Lag is ordered by the Bee-Hive Master Largo Lloyd to find out what Noir is up to, and he heads there with Niche and Steak. There he discovers a shell of what looks like a giant gaichuu, as well as a used cartridge which Noir left behind. Lag shoots his own shindan into the cartridge!

Lag visits the town of Blue Notes Blues, steeped in the legend of the Maka, the mysterious creature deeply connected to Niche. The people in town witnessed someone like Noir heading into a cave, however the Mayor, Khari Tonov, tells them that cave is where the Maka lives and is dangerous, and entry is forbidden no matter who it may be. But despite this, at Niche's suggestion, Lag heads toward the cave wanting to find out more about what Noir was up to.

200 years ago, Niche and her twin sister were shunned as cursed, and were eventually disposed of. Thrown into a river, with the most precious thing in the world, her sister, split apart from her, she matured all on her own, and has lived together with the Maka ever since. When Niche finally encounters her, she has no recollection of what happened, and instead protects Lag, a "human." Shocked by seeing her sister in such a state, she tries to kill both her sister and the other people. Lag tries to stop her, and shoots a shindan into her with his feelings...

With the wounded Niche left in the "Garden of Spirits" which the Maka protects, Lag runs into Zazie on his way back to the Bee Hive, and they stop by the town of Lament where Connor is. There, the two of them are surprised to find Connor collapsed, but it was because he'd eaten too many cookies from a nun named Sunny. Lag witnesses Roda, Noir's dingo, picking up a delivery of letters at the Abbey where Sunny lives, so he goes undercover and infiltrates the Abbey to find out if it is a Reverse base.

Sunny is ordered to put poison in the cookies that she bakes in the Abbey for Connor by the Abbess. Sunny is shocked at the order... Meanwhile, Connor is shocked when he sees Lag fighting with Roda and realises that the girl he fell in love with was actually a member of Reverse. And during all the confusion, a giant gaichuu Cabernet comes to attack!

The fight between Lag and Noir continues, and Zazie comes back to help after sending Wasiolka to report. Just then a ton of swarming type gaichuu, Lao-Lao, come to attack. Lag and Zazie do their best to fight the gaichuu, but the huge numbers and lack of dingos to back them up makes it a tough battle. But then a trusty ally appears, and finally it's time for Lag to shoot that Letter Bullet!

The Letter Bees are requested by the government to go after the Cabernet, as they still consider it a serious threat. With not enough personnel, the Sub Master of the Bee Hive and now office worker, Aria Link, heads out on a delivery herself. The letter is addressed to a Houdai Franklin, who was on the airship during the Day of Flicker and experienced that terrible accident. Since it's her first delivery in a long while, Niche tags along as her dingo, but the new duo has a tough time working together.

Aria and Niche final make it to Houdai's house. Aria tries to hand over the letter right away, but is injured when Houdai suddenly attacks her. But Aria doesn't flinch, and tries to convince him by talking about how a person dear to her lost something important on the Day of Flicker. Houdai hears this, lets them into his house, and begins to tell the story of his memories of the incident that happened on board that airship. At around the same time, Dr. Thunderland is treating Lag and Gauche, and the unthinkable occurs...

After the effect of being shot with Lag's letter bullet, Noir has awakened back as Gauche Suede. Lag asks Largo and Thunderland Jr. to allow Gauche to go home to the waiting Sylvette, and somehow gets permission for it. However, Largo and Thunderland Jr. can't help but shake off a certain feeling...

Torn apart from Noir, Roda chases after him to Yuusari Central, but when she sees Noir happily spending time together with Lag and Sylvette, she becomes distraught and her feelings fall into confusion. Just then, Roda is rescued from some men up to no good by Sarah and Hunt. Once acquaintances of Lag, Connor, and Zazie, they've begun living new lives in Central. Sarah works at an employment agency for "daily dingos" and when she hears that Roda used to be someone's dingo, she brings her to her workplace.

Garrard and Valentine, who came from Akatsuki, will go to any lengths to find Noir, even interrogating Sylvette. When Lag hears this, he tries to do something to make sure Sylvette doesn't get wrapped up in it all. However, Noir, now reunited with Roda, arrive at what was once a Reverse base. There, Garrard and Valentine along with Lag appear. Lag tries to bring Noir back with him, but he says that he is a member of Reverse and aims a gun at him...

Zazie finds out where the Cabernet ended up, but also finds a Reverse cell nearby at Shark Cape. There Zazie clashes with a Marauder who calls himself Jeel. Zazie shoots his shindan that consists of his malice, Blue Thorn, into Jeel, but Jeel's deep seated hatred for the Amberground government renders it ineffective and Zazie is cornered. On the other side, Lag heads toward Shark Cape after receiving word from Zazie, and encounters the leader of Reverse, Lawrence! Lag tries to shoot him with his shindanjuu, but for some reason he can't load any shindans...

The many Blue Thorn shindans Zazie shot into Jeel awaken the Cabernet. Just as Zazie thought, it takes Jeel away. However, while Zazie and Lag give chase to finish it off, they see the fragments of Jeel's heart. After knowing Jeel's real motivation, Zazie saves him despite himself. But the two of them are not going to waver from their hearts so easily...

Lag visits the city of Lament to see Connor, as he needs some ability to find the Cabernet which has buried itself into the ground. There, Connor is looking after Sunny, who had her heart eaten by the Cabernet. Lag reunites with Connor, and Sunny as well, but the Sunny that is there has none of the memories or heart of the Sunny that once was... But then, a smile pops onto her face, even though she was supposed to have lost all of her heart.

The plan begins to lure out the Cabernet, which has buried itself into the ground, with the recently recovered Connor. But they do not know where it is hiding, where it is heading, or what place it will resurface at. At the same time, Reverse's plans are reaching their final stage at last. In order to raise the strength of the Cabernet even further, Lawrence will use the fortified "hearts" of the ones who were unable to become spirit, and transports them all to the appointed place.

To stop Lawrence's plan and protect the ones who were unable to become spirit, Noir heads to the Bread and Weapon's Shop, Sinners. Noir asks Jacob, who is surprised to see him and worried, to give him a shindanjuu, and when he leaves the shop he runs into Sylvette. Sylvette is deeply worried, but pretends like she doesn't notice the changes in her brother. Noir is tugged back by those memories of Sylvette, but...

During the battle with the gaichuu, the ground underneath the Hill of Prayer suddenly collapses, and Lag and Noir fall down into the caves below. Lag tries again to return Gauche's heart, but...

Moc and Aria are prepared for the worst and are waiting at the Bee Hive for Lawrence, who came to see his evil plan come to fulfillment.

The ultimate battle with the most powerful gaichuu, the Cabernet, wrecking havoc in Yuusari central, comes to a close. Lag stands up, together with the Heart of all of the friends who he's received and become entangled with.