While playfully attempting to stab Mariam in the back with a wooden dagger, Elluka tells Mariam that she has no intention of staying in Lucifenia now that the king and queen had died. Mariam objects, saying that Elluka should stay since she is a great help to Lucifenia. Elluka decides that instead, she will train an apprentice. Ney interrupts, telling Mariam that Leonhart wants her to meet a new palace servant, Allen. Elluka leaves for Elphegort. Elluka arrived in Eldoh's Forest and meets her old friend, the Tree of Eldoh, to discuss the current events. Queen Anne has given birth to twins, resulting in a political dispute in whom should inherit the throne. Long ago, Elluka had found Riliane possessed by the Demon of Gluttony, and her Vessel of Sin is apparently incomplete. Elluka also dreamt of four visions:
Riliane was sent to the guillotine. The Lucifenian Royal Palace surrounded by armed people. Lucifenian troops attacking Elphegort. Mariam found dead in the palace courtyard. Confirming her third vision is the one that cannot be changed without interference, Elluka is prepared to flee Lucifenia if it happens. Eldoh merely states that Elluka doesn't want to see her acquaintances die, but rather give up everything and escape, just like when the Fire Disaster of Levianta occured. Elluka got angry and just as she is about to ask Eldoh for an apprentice, Eldoh goes to sleep. Getting more furious, Elluka kicks Eldoh, only to find herself being pelted by a pomegranate by Michaela and Gumillia. After making up, Michaela tells Elluka that she is interested in humans but she is not allowed to leave the forest. Elluka decides for herself to choose Michaela or Gumillia as her apprentice. Clarith then appears just after Elluka leaves. Having been hidden in the bushes, Elluka hears Clarith saying "I'm sorry that I'm alive." Although Elluka noticed Clarith was talking to herself, she realizes Eldoh may be right about her escaping cowardly. Elluka travels back to Lucifenia.
To disprove the humans that the "Stones of the Wild Spirits" is nothing but a myth, Michaela flies off to the Lake of Amusement in her robin form to pick Trauben Fruits despite Eldoh's orders not to leave the forest. However, a blackbird attacked her and she woke up in Clarith's home in Yatski Village. Michaela tried to escape but couldn't due to her injured wing, forcing her to leave herself in the care of Clarith and her mother. While her injured wing is healing, Michaela lived in a bird cage that Clarith made and she couldn't help but watch Clarith working with an unhappy face. The next day, Gumillia arrived in her chipmunk form to set Michaela free. Suddenly, Clarith’s mother arrived but kindly let them go. Michaela and Gumillia were surprised to find out that Clarith’s mother can talk with them directly. They saw that she was once a magician just like Elluka. Thanking her for her hospitality, Michaela returned to the forest with Gumillia.
Eldoh was furious with Michaela for disobeying his orders. After conferring with Gumillia, Michaela heartily apologized. Just as Michaela was about to share some of the Trauben Fruit she picked, Clarith suddenly appeared and started praying. Her mother has been ill for a while and will soon die, leading Clarith to beg for at least one friend in her life so that she wouldn’t be alone. Unfortunately, Eldoh was sleeping so he cannot hear her prayer. Michaela did and she was visibly upset.
A few days later, Michaela talked with Eldoh about Clarith. Eldoh tells her that even God shouldn’t be involved with humans. Elluka then appeared out of nowhere and pointed out that Eldoh was the one who assigned her to find the Deadly Sins. Elluka once again demanded for an apprentice, in which Eldoh finally agreed. Gumillia was to be Elluka’s apprentice while Michaela was chosen to find the Sin Fragments. Eldoh told Elluka that they are to return to the forest after three years. Michaela was confused that she was chosen but Elluka tells her that Eldoh might have other plans for her. Elluka then asks Michaela to think of a currently deceased woman. Michaela thought of Eve Moonlit.
The next morning, Elluka starts teaching Michaela and Gumillia, now in their new human forms, about the human world. Elluka also teaches Michaela how to sing a distinctive “Lu Li La” pattern to find the Deadly Sins while Gumillia was studying magic. After a whole month, Elluka tells Michaela to go to Aceid and start finding the Deadly Sins there. Michaela starts to feel sick so Elluka gives her some medicine to comfort her. Gumillia was getting very worried about Michaela going off on her own, but the two of them reassured that no matter what happens, they would come to each other’s aid.
While traveling to Aceid, Michaela's fever started to get worse and she ended up collapsing at the Tree of Eldoh. Michaela awoke once again in Clarith's house and while Clarith and her mother started treating Michaela, the elder of Yatski Village came in and demanded them to pay their rent since they didn't last month. Michaela intervened and paid off the debt with money Elluka gave her and asked Clarith if she can stay for a while. Michaela started working at a farm, taking interest in what humans do and learning more about Clarith. She was disturbed by the discrimination brought upon Clarith by the rest of the villagers except for Ein, whom Michaela befriended earlier. Clarith asked Michaela if she liked Ein, in which Michaela replies that she does not have any interest. Suddenly, another villager named Chelsea confronts Clarith, thinking that Clarith is making moves on Ein. Michaela reprimands Chelsea and in turn, Clarith and Michaela became friends.
One night, Michaela took a trip to a hillside alone. She then started singing a music box lullaby that Elluka taught her, finding out the location of the one of the sin fragments in a mansion somewhere in Aceid. Clarith found Michaela and the two of them started chatting, learning that Clarith's mother is not going to last much longer due to the Gula Disease and that Keel Freesis is the owner of that mansion. While walking home, Clarith found her mother collapsed in a bloody mess.
After Clarith's mother is buried, Clarith is all alone without anyone to be with her. Michaela then asked Clarith if she would like to go to Aceid with her and start a new life. Clarith refused, believing that Michaela is only being kind to Clarith because she only wanted to show off her beauty. Michaela protested, hugging Clarith and telling her that Clarith is a wonderful person, no matter what anyone says. Clarith bursted to tears, thanking Michaela and agreeing to go to Aceid with her. Suddenly, Ein enters and tells Michaela and Clarith that his father poisoned the elder's nephew, Eugen, and now is blaming Clarith for it. Ein helps Michaela and Clarith escape to Aceid and promises to bring Clarith's case to the village landlord, Count Felix.
Arriving at Aceid, Michaela and Clarith stayed at an inn run by immigrants. With money running out soon, the girls had to find jobs so Michaela decided to ask the Freesis family if they could hire them. Soon, Mikina dropped by the inn and Michaela had a pleasant conversation with her, eventually asking if she could hire her and Clarith. Mikina was willing to hire Clarith but not Michaela since she dislikes Elphegortians. However, Clarith defended Michaela, saying that she is a nice person. Mikina relented and agreed to hire them both. Michaela was assigned to wash clothes while Clarith took care of the eldest daughter, Yukina. Ein later visited them and told them that his father is arrested for false charges and that Count Felix has appointed Ein to be part of the army. Keel also arrived and greeted his daughter. Clarith very enthusiastically thanked Ein. He then left, although Michaela can see that Ein was crying.
After dinner, Michaela and Clarith finally have the chance to talk. Clarith's personality has really changed now that she has spent a lot of time with Yukina. As Clarith continued to talk more about Yukina, she figures out that Michaela was getting lonely and reassures her that she will always be important to her. Clarith then asks Michaela to sing again. Michaela does so and at the same time tracking down the Venom Sword in the warehouse. Keel arrives, having heard Michaela's singing and offers to hire a music tutor.
One day, Keel hosted a banquet with Michaela as the main attraction. Michaela sang for a while and afterwards met Kyle Marlon. Many nobles at the banquet have often asked for Michaela's hand in marriage. Mikina saw that Michaela was getting uncomfortable and told her to take a break. As Michaela finally relaxed in the empty living room, she couldn't help but notice a painting in the room: A portrait of a blond girl standing at the seashore.
While Michaela was examining the painting, Kyle approached her and told her that he was the one who painted that portrait. He then reveals that all he wanted to do was to be a painter but quitted because of his manipulative mother. Michaela then bluntly asked what is love since she never understood it, in which Kyle started giving his own opinion. Kyle then gave Michaela a shell necklace, telling her that he loves her. Michaela couldn't accept that, but she is willing to be friends instead. As Kyle left, Clarith saw what happened and told Michaela to stay away from other people. Michaela recalled Kyle's words and thinks that Clarith is becoming jealous.
While Kyle is staying over at the Freesises, Michaela learns from Keel that Kyle is engaged to Riliane. Michaela got angry with Kyle for deceiving her. Kyle explains to Michaela that his mother put him up to this and he only viewed Riliane like a little sister. He also says that Riliane isn't a bad person; it is only because she was raised like this. Michaela outright tells Kyle to not defy her mother's decision no matter what and that a monarch and a maid shouldn't be together. Kyle seems to understand and just as he is about to leave, he embraces Michaela suddenly and asks her if he ever abandoned everything, would she come with him. Michaela was left speechless. Just as Michaela was trying to take her mind off of it, she felt that the Vessel of Sin, which was originally in the Freesis warehouse, has been moved. Michaela found Keel in his room, who showed her the Venom Sword. Now knowing what the Vessel of Sin is, Michaela went out into the garden that night and sang a song, Recollective Musicbox, to inform Elluka.
While out shopping for soap, Michaela met an orphan who lost her parents to the same disease that claimed Clarith's mother. Michaela decided to sing for the orphan a song that his mother used to sing, South North Story. While Michaela was singing, a crowd formed and applauded just as she finished. As Michaela is about to leave, she is stopped by a blonde-haired boy, Allen Avadonia. After receiving a "very amazing spring onion" from him, Michaela rode in Allen's carriage on the way back to the Freesis Mansion. After sharing a few conversations, the two of them arrived there. Parting ways with Allen, Michaela returned to Clarith, who is slightly surprised that Michaela was meeting another male. After washing the laundry, Michaela overheard Gast Venom and two other members of his group, learning that they are after the Venom Sword as well.
Michaela then planted the spring onion in the ground, allowing her to communicate directly with Elluka. Michaela informs Elluka about her current situation, the Venom Sword's location, and Gast Venom's intentions. Although the Venom Sword has nothing to do with Riliane, Elluka orders Michaela to keep an eye on it and tells her that she knew Gast a long time ago. He was once Elluka's ally. Now, Gast is her enemy.
Suddenly, Keel gathers everyone together and tells them that Kyle has been placed under house arrest by his mother, Prim Marlon. Apparently, Kyle has announced his withdrawal from his engagement to Riliane, saying that he is in love with another woman with green hair. All attention is focused on Michaela, who is very dismayed by this. With the “Green Hunting” in the midst, Clarith, deeply caring about Michaela, vows to never leave her.
Michaela uses the spring onion again and learns from Elluka that the “Green Hunting” is already underway. Elluka and Gumillia have managed to escape and orders Michaela to flee back to Eldoh’s Forest so that she can be reverted back to a forest spirit. However, Michaela refuses, preferring to stay with the humans she had cherished. Elluka loses it, prompting Gumillia to speak up and just when Michaela is expecting a rebuttal, Gumillia reveals that she intends to remain a human as well to protect Michaela too. Elluka, further pissed, finally consents to both of their requests. Michaela then tells Elluka that she will be hiding in a well in the forest. Elluka promises to pick her up when everything is over.
Lucifenia has begun its attack on Elphegort, forcing Michaela and Clarith to flee. While Clarith is trying to calm down a distraught Yukina, Mikina gives Michaela her coat and dearly hopes that she will be able to meet her again. Michaela and Clarith arrived at what is left of Yatski Village, only to be caught by Lucifenian soldiers. Just then, Ein appears and rescues them. The three managed to arrive in Eldoh’s Forest. Clarith takes Michaela’s coat and intends to catch the army’s attention. Michaela begs Clarith not to do this but Clarith just embraces Michaela and tells her that she loves her. Clarith then kisses Michaela. Michaela suddenly falls unconscious, having been slipped sleeping pills by Clarith earlier.
Michaela wakes up in an underground shelter in a well, only to find Ein’s corpse in front of her. Weeping for her male companion, Michaela dragged Ein’s body and buried him under a tree before returning to the well. Allen finds Michaela and tells her that Keel and his family were imprisoned in Lucifenia but are safe for the time being. Allen leaves, vowing to help Michaela escape when the coast is clear. Michaela realizes that Allen is in love with her. However, Michaela sadly couldn’t return his feelings.
While hiding in the well alone, Michaela hears Allen’s voice telling her that it is safe to come out. Although the voice seems different, Michaela started climbing, only to be kicked off the ladder and injuring herself. “Allen” then throws off the disguise, revealing to be Ney Futapie. Laughing triumphantly, Ney drew her dagger and proceeds to stab Michaela in the chest.
As she lay there dying, Michaela is discovered by Allen. Cradling Michaela in his arms, Allen started sobbing, confessing his love to her. Michaela thinks about how Allen is just like Kyle, wanting to abandon everything for one person. Drawing her last breath, Michaela wishes for Clarith to be safe, the last thing she heard was Allen’s scream of anguish.
Daniel Ausdin, one of the Lucifenian soldiers, started interrogating Clarith on Michaela’s whereabouts. However, another person appears and tells Daniel to release Clarith, informing him that Michaela is confirmed dead. Clarith, shocked by the news, bites down on her tongue so hard it bled, causing panic among the soldiers and forcing them to rush Clarith to the hospital. Clarith is reunited with the Freesis family, although they were also saddened by Michaela’s passing. Keel has been talking with a swordswoman in red armor named Germaine Avadonia. Germaine asks Keel and Clarith if they want to join the resistance. Keel pledges his support but Clarith refuses. Keel tells Clarith that he and the rest of his family will soon be leaving for Marlon and invites Clarith to join him. Again, Clarith declines, preferring to work at a monastery.
While working at the monastery, Clarith couldn’t shake off Michaela from her mind. One day, Elluka and Gumillia paid a visit and handed Clarith a potted plant. Elluka explains that Michaela has been chosen by Eldoh to be his successor. As a result, Michaela had been transfigured into a tree sapling. Elluka entrusts Clarith in taking care of Michaela until she matures enough to be planted. Gumillia then casts a spell to conjure Michaela’s spirit. Clarith becomes overwhelmed with sadness and asks Michaela if her life will ever be happy without her. Michaela replies that Clarith needs not rely on her forever, to continue to live on her own. Clarith finally understands and the two of them confess their eternal love for each other. Michaela’s spirit disappears afterwards. Elluka then leaves and Gumillia informs Clarith that the Lucifenian Revolution is over and that princess Riliane was executed.
While Clarith is enjoying her time again with Michaela, the monastery is having a hard time with their newest convert, a blonde-haired girl named Rin. Clarith had found Rin collapsed and starving, prompting her to let her stay at the monastery. While watering the plants, Rin couldn’t help but notice one particular plant, not knowing that it is actually Michaela. Clarith tells Rin that this plant is her best friend and should be treated as such. Rin got really confused but nonetheless asks Clarith that if Rin had done horrible things, Clarith would still forgive her. Clarith promises that. Meanwhile, Michaela has been growing well and just as Clarith is about to lock the door to the confession room, she overheard Rin’s voice in there. It was then Clarith realized that Rin was in fact Riliane Lucifen d’Autriche. Overcome with revenge, Clarith followed Rin silently, reaching the beach. Rin threw a message inside a bottle out to sea and just as Clarith is about to stab her, she saw a vision of two people. The first was a boy who looks exactly like Rin. The second looks like Michaela but has an evil expression. Rin noticed Clarith with the knife and closed her eyes, preparing herself for the end. Clarith wanted to kill Rin for having Michaela killed but she couldn’t shake the fact that Rin is lonely and sad, just as she once was. The knife swung down.
Kyle remembers that Keel had shown him the Venom Sword, somehow causing him to have lustful feelings. A soldier then informs Kyle that Germaine and the rest of the rebels escaped. Kyle then believes that Germaine has something to do with Michaela’s death. Gumillia reveals that after the Freesis Mansion burned down, she and Elluka managed to retrieve a number of priceless works of art belonging to Keel. Next, the two of them secured Michaela’s body after “beating up” Kyle. Michaela’s body then became like roots. Elluka then bartered with Keel for the Venom Sword, only to find the Demon of Lust not inside it.
Clarith and Rin brought Michaela over to the forest to be planted. Clarith apologized to Rin for cutting her hair. Rin merely brushed it aside, saying that she liked the look anyway. She then asked Clarith if she could teach her how to make brioche. Clarith promised as compensation. After planting, Rin said a prayer to Michaela and started crying. Clarith followed suit and like this, the two of them cried until nightfall. Eldoh continues to wonder why they are crying.