The central twist of "Wolfwalkers" is Robyn's transformation. After being accidentally bitten by Mebh, Robyn discovers that she too has become a wolfwalker; her spirit leaves her body as a wolf whenever she sleeps. This fundamentally changes the film's conflict, turning her from a hunter into the hunted and placing her in direct opposition to her father and the Lord Protector.
A major plot point revolves around the fate of Mebh's mother, Moll. It is revealed that the Lord Protector has not killed her, but has captured her wolf form and keeps her in a cage in his castle, intending to display her as a symbol of his power to tame the wild. Mebh, defying Robyn's warnings, enters the town to free her mother, leading to the film's climax.
In the final confrontation, Bill Goodfellowe is faced with a choice between his duty and his daughter. As the Lord Protector is about to kill Robyn's wolf form, Bill transforms into a massive wolf himself, having been bitten by Moll earlier during the chase. He fights and defeats the Lord Protector, who chooses to fall to his death rather than be turned into a wolfwalker. The magic of the pack, now including Robyn and Bill, is able to heal Moll's near-fatal gunshot wound. The film concludes with the newly formed family—Robyn, Bill, Mebh, and Moll—leaving Kilkenny behind to find a new home in the wild, fully embracing their new lives.