In 1650 Ireland, the residents of the town of Kilkenny are attempting to clear the neighboring woods for farming as per the orders of the authoritative Lord Protector Oliver Cromwell, putting them at odds with a pack of wolves living within them. Hunter Bill Goodfellowe and his young rebellious daughter Robyn have been summoned from England to Kilkenny by the Lord Protector to help exterminate the wolves so the woodcutters can continue their work unimpeded. Disliking the confining nature of Kilkenny and wanting to help Bill, Robyn decides to sneak out of the town one day to follow him along with her pet falcon, Merlin. After accidentally shooting Merlin with her crossbow after trying to kill a wolf attacking a shepherd and his flock, Robyn watches as a mysterious girl takes Merlin with her back into the woods with the retreating wolves. The Lord Protector scolds Robyn for not working in his scullery and gives Bill two days to kill the wolves.As she is escorted back to Kilkenny by the Lord Protector's guards, Robyn manages to sneak away back into the woods, where she finds Merlin has miraculously healed. She is then approached by a young wolf, causing her to stumble into a trap. As the wolf attempts to free Robyn, she attempts to attack it, causing the wolf to bite her on the arm. Merlin and the wolf lead Robyn back to the wolves' den, where she discovers that the wolf is the same mysterious girl from earlier. The girl, Mebh, calls herself a "wolfwalker" and she magically heals Robyn's wound "before it's too late." As Mebh and the other wolves lead Robyn out of the den and woods, the two girls get to know more about each other, and they quickly bond over their desires for freedom. Robyn also learns that Mebh's mother, Moll, also a wolfwalker, has not yet returned in her search for a new home for her pack. Robyn tries to convince Bill about the existence of wolfwalkers and her plans for a nonviolent way to rid the woods of the wolves, but Bill ignores her, upset over her disobedience of the Lord Protector's orders.The next morning, while working her first day in the scullery, she is drawn into the Lord Protector's chambers by a mysterious voice as well as the wolfwalker magic residing in her bitten arm, discovering a large concealed cage, though is quickly ushered out by the head maid. That night, while she sleeps, Robyn finds her soul has left her body and transformed into a wolf, thus making her a wolfwalker herself, forcing her to flee Kilkenny. Returning to woods, Mebh is ecstatic to learn of Robyn's transformation, and she helps Robyn get accustomed to her new form, including her heightened sense of smell, sound, and speed.Upon returning to Kilkenny, Robyn attempts to return to her human body, but is drawn to the presence of another wolfwalker, suspecting it to be Moll. After evading the frightened townspeople, Bill amongst them, Robyn manages to infiltrate the Lord Protector's manor, where she finds Moll. Despite assuring her that Mebh is unharmed, Moll tells Robyn to instruct Mebh to leave the woods with the pack, as it is no longer safe for them there. Unable to free Moll but able to evade the Lord Protector, Robyn manages to return to her human form just as Bill returns home, though the Lord Protector and the rabid townspeople arrive shortly after. The Lord Protector gives Bill one last chance to rid the forest of the wolves lest he be demoted as a foot soldier in his army, and he assures the townspeople that he can tame the wolf that he's captured, and by extension, nature itself. Robyn's pleas to let Moll go and declaring her a wolfwalker fall on deaf ears, the Lord Protector deeming it "pagan nonsense."Fearing separation from each other, Robyn and Bill tend to their usual duties. Mebh, waiting for Robyn to return on a promise from the previous night, infiltrates Kilkenny herself and searches for her mother. She finds Robyn, who attempts to relay Moll's message about taking the pack and leaving with them, but Mebh, hurt by Robyn's refusal to help rescue her mother, resolves to do so alone. Mebh and Robyn then watch as the Lord Protector presents a muzzled and chained Moll to the townspeople. An enraged Mebh storms the stage and attempts to free her, and when Bill tries to restrain her, Moll breaks the muzzle and bites him on the arm. After placing Moll back into the cage, Mebh is forced to flee, but not before promising to return with her pack to rescue her mother. The Lord Protector orders Bill to kill Moll before he joins him and his army to wage war on the wolves. Robyn protects Moll from Bill before freeing her and reuniting her with Mebh before she and her pack can attack Kilkenny, earning Mebh's forgiveness.Bill arrives and shoots Moll in the chest, fearful for Robyn's safety, though he witnesses Moll's wolf form turning into a spirit and leaving to return to her human form in the den, Mebh and the wolves following it. Robyn transforms into her wolf form and follows them just as the Lord Protector and his army arrive and begin razing the forest. As Mebh works on trying to heal a grievously wounded Moll, she sends her pack to follow Robyn, who leads them to attack and hold the army back to prevent them from reaching Mebh and Moll. Mebh summons Robyn and her pack back, realizing she needs them present in order to heal Moll, though Robyn is caught in the blast of a cannon ball attack, causing her to get left behind. Robyn thwarts another cannon attack aimed at the den, but is injured as a result. Before the Lord Protector can kill her, Bill, due to Moll's bite, becomes a wolfwalker and attacks the Lord Protector in his wolf form. Bill, with help from Robyn in her human form, overpowers the Lord Protector and holds him over the edge of a cliff above a waterfall. The Lord Protector resigns to his fate and willingly plunges himself into the jagged rocks below.Robyn and Bill manage to return to the den where they both help Mebh and the pack revive Moll, who invites Bill and Robyn to stay with them and embrace their new identities as wolfwalkers. Robyn, Mebh, Bill, and Moll then travel with their pack to find a new home, riding in a wagon drawn by the Lord Protector's horse. Bill puts a flower in Moll's hair and Mebh and Robyn fall asleep in the back, their wolf forms running around the wagon.