Hilda, her mother Johanna, and their deerfox Twig, have lived in the wilderness ever since Hilda was born. During one of her adventures, she encounters a troll and removes the bell she had tied onto its nose earlier. Later that day, their house is threatened by small, invisible creatures. Johanna insists they move to Trolberg, but Hilda is determined to fix things so they can stay. She learns that the invisible beings are elves, and she befriends one named Alfur, who arranges a meeting with the prime minister. Despite Hilda's efforts, she learns that only the king can turn things around. Hilda feels dejected, but soon feels better when Alfur decides to take her to the king, even if it violates protocols.

That night, Hilda meets the giant from the previous episode, who explains to her that he is waiting for a friend. The next day, Hilda and Johanna visit Trolberg. Hilda is still reluctant about moving, but Johanna tells her to keep an open mind. The Wood Man visits their house and lends her a book about giants, leading Hilda to realize that the giant she encountered was Jorgen, who resides from the highest mountain in the north. The next day, Hilda and Alfur set out to find the Elf King. Unfortunately, to Hilda's anger, he retreats in panic when he sees her. Hilda lashes out, only to be interrupted by the wakening of the mountain, which appeared to be another giant sleeping under layers of snow and soil. Hilda catches the royal palace in time and realizes that this giant is who Jorgen is waiting for. The two giants reunite and just as Hilda and Johanna are free to live in the wilderness once more, Jorgen crushes the house as they walk off to space. A horrified Johanna and Hilda realize they must move to Trolberg now that they know how hard it is for elves to live by other bigger creatures. Johanna, Hilda, Twig, and Alfur head off to Trolberg and settle into their new home.

As the city prepares for The Bird Parade, an annual festival to honor The Great Raven, Hilda goes out and attempts to make friends. She spends the day with a group of bullies and is appalled when they begin throwing rocks at birds. One bird gets injured and Hilda brings it back to her apartment. She and Alfur try to speak with the bird, but he has amnesia. The only thing he remembers is needing to find a statue. Before heading out to watch the parade, Johanna discovers the bird and forces him outside. It is revealed that he is The Great Raven, whose job is to bring good fortune to the city. As Alfur and Raven try to find the statue, Trevor finds and captures him, tries to get him to talk and accidentally pushes him into the river. Hilda arrives in time to see the birdcage going underwater, but she manages to remind him that he is the Great Raven. Hilda jumps to the river to save the bird, but with his memory restored he transforms into his larger form and carries Hilda into the sky above the city. He reveals to Hilda that years ago, he landed on the statue, and the people thought he was the messenger of their god. The harvest was bountiful that year and the people believed it was his doing, so they started the festival in his honor. The year he missed the festival was bad, but it has nothing to do with bad luck. He wanted to give the city hope, so he continues coming to the town every year, even though he is not the Great Raven, he is a thunderbird. With everything settled and the parade started back up, Johanna takes Hilda to a special place so they can watch the parade together. Hilda confesses that she might like the city after all.

On their way to parents' night, Hilda and Johanna meet Principal Magnusson, who is very excited about the grand finale, a dedication ceremony for the school's new statue of one of Trolberg’s great founders, Edmund “the Troll Slayer” Ahlberg. During the event, Hilda presents her nittens collection and David presents his collection of rocks. Hilda’s teacher, Ms. Hallgrim, asks the students to close the curtains and play a video about the history of the school, but soon after the video starts playing, the projector falls to the floor. David’s collection of rocks also appears to be on the floor and Ms. Hallgrim locks up the rocks, assuming that it was Hilda who threw the rocks into the projector. Frida and David tell Hilda that Ms. Hallgrim thinks Hilda is a problem student and wants to transfer her to a class for students with behavioural difficulties.

To earn the Botany Badge, Hilda suggests finding a rare plant that David once saw. It turns out that this plant grows near a settlement of elves, who immediately start an attack. The elves capture David, but Hilda and Frida manage to escape. They learn from Alfur that these elves - the Lost Clan - were banished by the King of elves for an error made during the execution of a plot of land sale contract. Alfur offers to complete the contract, but the elves declare that they don't use contracts anymore, instead taking their word for it or fighting, leaving Alfur (who is a descendant of the family that also signed the contract) to fight ten elves. Frida asks for a delay to find a loophole in the contract, while David remains a hostage of the elves.

For the second year in a row, due to various setbacks, David is unable to audition for the Warblers, and Johanna cannot find a job as a graphic designer in Trolberg, so she takes a job in a store. Hilda goes to the library with Twig and wants to find a comfortable place to read a book. Twig scratches a shelf, causing Hilda to find a hidden storage of books, among which she notices "How to Aid and Keep Thy Friends Forever" book. Among the tips there is a magic spell "how to ensure a friend's success in a chosen endeavor". The librarian^{[lower-alpha 3]} enters the room and says that this book is for internal circulation only, so Hilda makes a copy of the page and runs to her apartment. For the spell, she immerses David's hair and his musical instrument in a tide pool, and the next morning she finds a mouse there, which she discreetly brings to David. David passes the audition with flying colors. Inspired by her success, Hilda works the same spell with Joanna and she is soon hired as a graphic designer to create bells advertisements.

Hilda and her friends manage to escape from the Black Hound, but Hilda is still worried about Tontu. She asks around the city, only to find that many other nisse have been mysteriously expelled from their home. On the way to the Sparrow Scouts badge ceremony, she finally finds Tontu safe and sound, who decides to explore the Nowhere Space inside the scout hall. During the ceremony, the Black Hound comes out of Nowhere Space and Hilda and Tontu flee, ending up in Hilda's home. Her house's nisse appears to defend its territory, only to realize that the hound was actually its pet, Jellybean. Hilda also figures out that it was actually Jellybean that had been messing up everyone's houses by travelling through Nowhere Space. After finding out that Jelly Bean is innocent, Hilda, her mum, and the two nisses must run from Trolberg's safety patrol. While driving, the group is separated while using Nowhere Space to warp out of the city, sending Jellybean and his owner into the wilderness. Hilda and her mum return home, with Tontu taking up residence there as well.

Victoria Van Gale has turned over a new leaf after the destruction of her Weather Station (110 'Storm') – she's moved to Trolberg and has set up a sanctuary for displaced wildlife in an abandoned windmill. Hilda and Frida pitch in to help but David remains deeply suspicious, a rift that tests their friendship. David is right – the windmill is a front for a dangerous experiment that will allow Van Gale to exploit Nowhere Space. Hilda, David, and Frida must band together to keep her from causing a catastrophic rip in Nowhere Space.

Twig feels left out by Hilda. One night he sees lights in the sky and runs away through the gates of Trolberg. On his way to the lights he is chased by a wolf-like creature. Hilda and mum track Twig down through the wilderness, flashing back to memories of Hilda and Twig's first encounter, when Twig was trapped under a pile of stones and Hilda helped him to get out. Hilda and mum reach a cliff and another flashback shows Twig saving Hilda from falling off the cliff. When Hilda and mum start ascent, Hilda is attacked by the wolf-like creature. The situation seems hopeless, but Twig comes to save Hilda; the creature falls off the cliff.

At Trolberg's 'Winter Festival', Hilda encounters a group of strange little men called 'Yule Lads' who are looking for naughty children. They're funny and fun to have around, but Hilda realizes too late that they are servants of the Gryla; a legendary monster that eats misbehaving children. With the hungry Gryla fast approaching, Hilda and the Yule Lads must work together to cook up an alternative (vegetarian) holiday feast for it to eat.

Johanna catches Hilda trying to skip out on her curfew using Nowhere Space, and their struggle causes a 'tear' that transports them to the mysterious 'Stone Forest'. They search for a way out, avoiding trolls along the way. Meanwhile, David and Frida leave Trolberg to search for Hilda. Their paths cross with Ahlberg and Gerda after a spectacular dirigible crash, and the group sets up camp on the base of a mountain. Hilda and Johanna are stranded in the 'Stone Forest', David and Frida are stranded on the mountain, but they are closer than they realize...

Hilda and Johanna have escaped the 'Stone Forest' only to discover that Twig has been taken captive by the Two-Headed Troll. They stage a daring rescue that triggers an all-out brawl between the trolls. Escaping the chaos, they are given shelter by a friendly Mom and Child troll, who use Troll Magic to lead them on a path out of the forest. Meanwhile Frida, David, and Gerda survive a night on Troll Mountain, and construct their 'floating life raft'. Hilda and Mum's escape takes a terrifying turn when they are cornered by the angry Two-Headed Troll. But Alfur shows up on pigeon-back just in time to rescue them and lead an aerial escape from the mountain.

Finally, back at home, Johanna tucks Hilda into bed safe and sound for some much-needed rest. But the next morning, as Johanna brings Hilda breakfast in bed, she discovers that Hilda is gone. In her place, the Troll child peeks out from the covers...

Hilda has found herself stranded in troll country with the body of a troll. She goes on a quest to change back into her human form and reunite with her mum. Other trolls bring her deeper into their world: their customs, their cuisine, and their legends; namely the infamous Mountain King. Meanwhile, as tensions rise between the gathering trolls and the city of Trolberg, Hilda's mum scours the mountainside desperate to find her daughter before the conflict erupts into a full blown war.

Continuing from the last episode, it's revealed that Anders is alive and stuck in the fairy mound in Tofoten. Hilda, Frida, and David head to the mound to rescue him, with Johanna not far behind. Hilda goes inside the mound and comes across a boat that ends up leading her to where her father is, alongside Victoria Van Gale. Both of them escape, but when it's revealed that Johanna went in to find her, Hilda goes back in to rescue her.

Back in the mound, the world around Hilda has changed. She ends up unknowingly coming across a young Johanna, and tries to help her find her parents. When they manage to find them, Hilda realizes she's part fairy. Johanna's parents tell the story of what happened to them. When Johanna became sick with an unknown disease, her parents made a bargain, saying that in order for Johanna to remain healthy, she must be sent to the fairy world in 10 years. Not wanting this, her parents went in her place instead, with Astrid taking care of her. Seeing as how mother and parents are reunited, Hilda and Johanna are no longer allowed to leave, which devastates the former.

Back in Tofoten, Frida and David ask Twig to help them find Hilda. Twig, with help from the former, howls for his pack. Meanwhile, Hilda, realizing that while humans can't teleport between worlds, creatures can, as they were booted off. Noticing that Twig is coming to rescue them, Hilda and an initially reluctant Johanna decide to try and escape the fairy world. Astrid heads to the person that her brother bargained with, asking them to let Hilda and Johanna leave in exchange for her life. Just when it seems like they won't make it, Johanna starts to fly, and they manage to make it back to the human world with the help of Twig's parents.

On Earth, Johanna initially feels very sick, but soon recovers, as she and Hilda believe that Astrid gave her life to save Johanna's. At Astrid's home, it's revealed that she's alive, but has been banished from the fairy world for talking back to the bargainer. As it turns out, Van Gale discovered how to travel through portals and wanted to make a bargain. They head inside, with Hilda happy that everything is okay.

An epilogue occurs during the Bird Parade, with Anders finding an apartment and the Great Raven returning.