The citizens of a once-peaceful medieval kingdom are thrown into chaos when an unexpected attack occurs from the Great Black Monster. A thousand years prior, the revered Gloreth emerged as the hero who defeated this fearsome creature and established protective walls around the kingdom, ensuring peace for generations. This protective measure was institutionalized through the Institute for Elite Knights, where only the descendants of knights, including Ambrosius Goldenloin (Eugene Lee Yang), can be knighted.
Fast forward to the present day, and the kingdom has embraced advanced technology. Ballister Boldheart (Riz Ahmed), a commoner and the first of his kind to be knighted by Queen Valerin (Lorraine Toussaint), is about to undergo the knightly ceremony alongside his partner, Ambrosius. However, during the ceremony, an accidental laser discharge from Ballister's sword tragically kills the Queen, leading to chaos. In the midst of the turmoil, Ambrosius grievously cuts off Ballister's arm, resulting in the latter’s escape and subsequent status as a fugitive.
As Ballister flees the scene and creates a prosthetic arm, he's approached by Nimona (Chloë Grace Moretz), a shape-shifter who understands what it means to be an outcast. Believing she detects a "villainous spirit" in Ballister, she offers her assistance in seeking revenge against the elitist society that has wronged them both. Despite her insistence that he embrace his villainous side, Ballister firmly maintains that he is neither a villain nor a murderer.
In a desperate attempt to clear his name, Ballister tries to confront Ambrosius but is captured instead, and he quickly realizes no one is willing to hear his side of the story. Nimona, employing her unique abilities, helps him escape from the dungeons while transforming into various creatures to fend off the palace guards. They plot together to kidnap Diego the Squire (Julio Torres), who possesses crucial evidence pointing to the Director of the Institute (Frances Conroy) as the true culprit behind the Queen's murder.
After obtaining video evidence from Diego, they confront Ambrosius and the Director. However, the Director deftly manipulates the situation, leading to her knights destroying their only proof. In a moment of betrayal, Ambrosius, under the Director's influence, arrests Ballister, which prompts Nimona to create yet another chance to escape.
Tensions heighten as the Director's manipulation unfolds; she admits to framing Ballister and killing the Queen due to her fear of societal change. But a shocking revelation occurs when Ambrosius is revealed to be a disguised Nimona. Following this twist, Ballister captures the Director's confession, which he broadcasts, igniting public outrage. Alarmingly, the Director flexes her power, skewing public perception by declaring that Ballister has exploited Nimona's abilities.
Ballister, feeling betrayed, confronts Nimona about her deceptive actions, igniting a heated argument that results in her fleeing into the woods. Heartbroken, she reflects at a well where she once encountered Gloreth, recounting her history as a misunderstood being forced to hide her identity. In a pivotal moment of despair, she transforms into the Great Black Monster once more, contemplating her own demise by attempting to impale herself on Gloreth’s statue.
Just as she is about to commit the act, Ballister intervenes, apologizing and embracing her, leading to a heartfelt reconciliation witnessed by the kingdom's citizens. In a desperate attempt to eliminate Nimona, the Director authorizes a devastating laser cannon aimed at her; yet, even in her final moments, Nimona transforms into a massive phoenix-like creature to save the kingdom, resulting in her apparent death along with the Director's demise.
As time passes, the kingdom begins to heal and adapt to new changes as the barrier once dividing it crumbles, allowing citizens to travel freely between worlds. In a twist of fate, Ballister and Nimona are celebrated as heroes, and their bond with Ambrosius is mended. Ultimately, a renewed hope flourishes as Ballister hears Nimona's voice, discovering she has survived against all odds.
