Picking up where season one left off, the unconscious Lag is transported to the Bee Hive.
Lag and Connor search for Niche, but after a series of strange events and misunderstandings, Niche ends up rescuing Lag.
Lag is asked to find out who sent Ray pictures of hydrangea-colored mountains. These letters remind her of her childhood and help her find strength to fight her illness.
Lag is seeing things...a four-eyed creature to be exact. The strange illusions continue to ensue until Lag uncovers that they are somehow based in reality.
Many incidents are reported of Reverse Marauders attacking Bees.
While Lag pursues a thief, Sylvette goes after Autobahn who has taken control of a carriage in order to escape.
Lag and Niche go out of town to find Noir. While trying to stay hot on Noir's trail, Lag discovers an unusual gaichuu.
The people of Blue Notes Blues lived in peace with the Maka until sin corrupted the hearts of man. Later, Lag discovers that Noir has entered a cave, which is a path leading to Blue Notes and the holy site.
Lag and the townspeople are attacked by Niche. When Lag shoots Niche's sister, it is revealed how he met Niche and how their friendship developed.
Lag learns that spirit insects were "chosen ones," born of small insects and spirit energies. But as their hearts shed away, they become gaichuu. When that happens, they will bring peril to the land.
The nuns head for the prayer hill, and Sunny is ordered to poison Connor. Later, Connor investigates claims against Reverse and finds Lag fighting Roda, who takes him hostage.
When Roda continues to fight with Niche and Lag, she is floored when Lag saves her.
Per a request by the government, Largo puts Zazie in charge of the personnel that will destroy the Cabernet. Later, Lag undergoes examination by Dr. Thunderland, Jr.
In a Flashback, Franklin reveals the details behind the Day of Flicker.
Lag's request to allow Gauche to come home is denied. Largo and Dr. Thunderland seek to know how Gauche has regained his lost heart as well as what happened during his time in Akatsuki.
A flashback reveals what happened after Roda survived her fall.
When capital inspectors come to interrogate Sylvette, Lag impersonates her. Meanwhile, Largo gets a tip that there are Marauders around Yuusari.
There's a possibility that Noir has been using Lag's memories of Gauche as a deceptive device. Later, Aria learns that the light from Akatsuki can cause people to lose their hearts.
Lag learns that, despite his intent to deliver people's hearts, it is the government who has stolen them.
Worried that the gaichuu may attack, Zazie seeks to use Connor's dingo to locate them.
Lag vows to defeat the Cabernet and bring back Gauche's heart. Largo leaves on a business trip, and Dr. Thunderland looks after Sunny, who is recovering at the Bee Hive.
Having escaped Lawrence, Noir sets out to acquire a shindanjuu; meanwhile, Roda and the others who couldn't become spirits are taken to a dark place.
Gauche has unexpectedly saved everyone from the gaichuu.
The gaichuu are not phased by the attacks from Lag, Noir, and Zazie. Later, the Cabernet rampages through the city and the final battle ensues!
Noir is severely injured. Lag uses all his strength to issue a fatal shot to the gaichuu. Later, everyone tries to continue living their lives as normally as possible.