Plot

When a knight in a futuristic medieval world is framed for a crime he didn't commit, the only one who can help him prove his innocence is Nimona -- a mischievous teen who happens to be a shapeshifting creature he's sworn to destroy.

When Ballister Boldheart (Riz Ahmed), a knight in a futuristic medieval world, is framed for a crime he didn't commit, the only one who can help him prove his innocence is Nimona (Chloë Grace Moretz), a mischievous teen with a taste for mayhem - who also happens to be a shapeshifting creature Ballister has been trained to destroy. But with the entire kingdom out to get him, Nimona's the best (or technically the only) sidekick Ballister can hope for. And as the lines between heroes, villains, and monsters start to blur, the two of them set out to wreak serious havoc - for Ballister to clear his name once and for all, and for Nimona to...just wreak serious havoc.—Netflix

The citizens of a medieval kingdom were attacked by the Great Black Monster, without warning. The Kingdom was peaceful, and the citizens were happy until the Monster attacked. A hero in form of Gloreth came forward who vanquished a "Great Black Monster" and enclosed the kingdom with a high wall one thousand years ago.

The Kingdom is now protected by the Institute for Elite Knights, established by the legendary heroine Gloreth (Karen Ryan). Gloreth decreed that the descendants of the Knights would protect the Kingdom for generations to come. After 1000 years, the Kingdom has now embraced futuristic technology.

Ballister Boldheart (Riz Ahmed), along with his fellow knight and boyfriend, Ambrosius Goldenloin (Eugene Lee Yang), is about to be knighted. Ballister is the first commoner to become a knight, as Queen Valerin (Lorraine Toussaint) is trying to change tradition so that "anyone can be a hero". Up till that point, only descendants of Knights could be Knighted by the Queen. Ambrosius is a direct descendant of Gloreth himself. Ballister was given his sword by the Squire named Diego, before the warriors are brought into the arena where the Knighting ceremony would take place.

During the ceremony, a laser shot from Ballister's sword kills Valerin. The laser was activated automatically, when the sword was in Ballister's hands and was pointed towards Valerin. A distraught Ambrosius ends up cutting off Ballister's right arm. Ballister escapes the arena in the chaos and a manhunt ensues as Ballister becomes a fugitive from law.

As Ballister hides and crafts a prosthetic replacement arm, he is visited by a shape-Shifter named Nimona (Chloe Grace Moretz), who has faced persecution for her powers. Seeing a "villainous spirit" in Ballister, as he is facing similar treatment for his commoner origin and the murder of the Queen, Nimona declares herself to be his sidekick. Nimona says that she can help Ballister take revenge against the elitist society that rejected him. Ballister insists that he is not a villain or a murderer. Ballister goes to meet Ambrosius to clear his name but is arrested instead. Ballister realizes that nobody is even willing to listen to his side of the story. Nimona helps Ballister escape the dungeons. Nimona has magical abilities that allows her to walk in and out of anywhere as she pleases. As Ballister is attacked by the palace guards, Nimona shape shifts into a Rhino and many other animals and defeats everyone.

Nimona takes Ballister to his hideout. Ballister realizes that Nimona is a shape-Shifter, but also concedes that he needs her help to prove his innocence. Nimona wants Ballister to fully embrace his villain personality, but Ballister keeps insisting that he is not a villain. Ballister and Nimona enter the city, where Ballister it tracked by Ambrosius. Only Nimona helps Ballister escape with her shape shifting abilities. To clear Ballister's name, the duo kidnaps Diego (Julio Torres), the squire who gave him the sword. Diego gives them video evidence revealing that the Director of the Institute (Frances Conroy) is the murderer. While taking the evidence to Ambrosius, Nimona tells Ballister to question everything he has been taught. She asks what the walls around the city are supposed to stop. The duo confronts Ambrosius and the Director (who was with Ambrosius at that moment) with the evidence, but the Director manipulates her knights into destroying the evidence. Ballister asks Ambrosius to believe him, but Ambrosius orders his Knights to arrest Ballister, promoting Nimona to shape shift and engineer another escape.

Later, Ambrosius confronts the Director, who stabs him and admits that she framed Ballister and murdered the Queen, as she objected to the Queen revising tradition by allowing commoners to become knights, fearing that doing so would lead to the kingdom's downfall. However, "Ambrosius" turns out to be a disguised Nimona. Ballister records the Director's confession, then posts it online, leading to public outcry.

The Director discovers through ancient scrolls that Nimona is the Great Black Monster defeated by Gloreth. She uses this to convince the public that Ballister used Nimona's powers to fake the confession. The real Ambrosius meets with Ballister and reveals Nimona's past, insisting that Nimona deliberately deceived Ballister. Shocked by the revelation, Ballister argues with Nimona and questions their friendship (he says that Nimona used him to portray him as a villain, as Nimona was alone and needed companionship); feeling betrayed, Nimona flees into the woods.

Stopping at an old abandoned well, Nimona reminisces about her past: a thousand years ago, she wandered the world and turned into other animals to try and fit in with the wildlife, but none of the creatures she encountered accepted her. One day, she sees Gloreth as a child by the same well and turned into a human for the first time. After seeing Nimona, Gloreth immediately welcomed her and the two became best friends, and Gloreth was accepting of Nimona's powers. However, the other citizens of Gloreth's village, including Gloreth's parents, believed Nimona was a monster after discovering her shape-shifting abilities. The villagers attacked Nimona with torches, which accidentally set the village on fire. A confused Gloreth became hostile toward Nimona. Since that day on, Gloreth fought Nimona, in the shape of the Great Black Monster.

With Ballister's abandonment and Gloreth's betrayal echoing in her head, a distraught Nimona transforms into the Great Black Monster. She then enters the city, deciding to commit suicide by impaling herself on the sword of Gloreth's statue. The Director misconstrues this as an attack on the city and opens fire on the Monster. However, before Nimona can kill herself, Ballister stops her and apologizes to her, causing Nimona to change back to human form as they embrace and make amends.

The kingdom's citizens see this and are moved by it. Meanwhile, the Director, unmoved, orders a laser cannon to be fired from the wall to kill Nimona; Ambrosius protests, knowing that firing the laser into the city will kill innocent civilians. The Director then turns on them using the same laser she used to kill the Queen and prepares to fire the cannon herself. To save the kingdom, Nimona assumes a giant, red phoenix-like form and flies into the cannon, resulting in her apparent death, as well as the death of the Director. The resulting explosion destroys part of the wall, revealing a beautiful, mountainous valley behind it.

Sometime later, the kingdom undergoes several changes: the breach in the wall has become a passageway through which citizens travel freely, Nimona and Ballister are honored as heroes, and Ballister's relationship with Ambrosius has been restored. Ballister visits his old hideout. He hears Nimona's voice, and joyfully realizes that she has survived.