Code Geass: Nightmare of Nunnally

Code Geass: Nightmare of Nunnally is a manga spinoff of Code Geass: Lelouch of the Rebellion that is set in a different universe.

Though some of the basic plot points remain the same, the storyline revolves around Nunnally, Alice and Nemo instead of Lelouch, Suzaku and C.C.. One of the key differences is that people can be born as "Wired", meaning that they have a latent Geass ability without forming a contract, though they can still gain an additional Geass ability through a contract. Lelouch's Geass is also different in this spin-off as instead of absolute obedience he has the power of invulnerability, gained through a suit of black armor that resembles a more heavily padded version of his wardrobe as Zero in the original series.

Plot
Nunnally Lamperouge is a blind and wheelchair-bound girl who was once Nunnally vi Britannia, a princess of the Holy Empire of Britannia, until she was exiled to Japan with her older brother Lelouch. Years later, when Japan is conquered and renamed Area 11, Lelouch is caught in a terrorist attack by Japanese rebels in the Shinjuku ghetto, where encounters a girl named C.C. and disappears with her before an explosion destroys the area.

Worried about her brother, Nunnally attempts to investigate the Shinjuku as the governor of Area 11, Clovis la Britannia, orders all the ghettos to be destroyed to hide C.C.'s existence. As Nunnally gives into her rage and despair that Britannia has taken everyone she loves and left her helpless in the world, a strange doll with a Geass symbol on it emerges. The doll, named Nemo, offers Nunnally the power to make Britannia pay for taking everything away from her, but in exchange, Nunnally must fulfill Nemo's wish. When Nunnally accepts the contract, Nemo fuses with her, causing a humanoid Knightmare Frame to appear in a flash of light, and grants Nunnally's revived body the ability to "read the lines of the future".

As per their contract, Nemo tells Nunnally that from now on she will protect Nunnally as her knight. From there on, Nunnally and Nemo work together to discover Lelouch's whereabouts while fighting various enemies such as the Britannian Special Honorary Foreign Legion "Irregulars", honorary Britannians with Geass powers; and the Order of the Black Knights, led by the mysterious masked man Zero.

Nunnally Lamperouge
Nunnally Lamperouge is the main protagonist of this manga, and younger sister of Lelouch vi Britannia and Rolo vi Britannia. A former princess of Britannia, she enters into a Geass contract with the entity known as Nemo, and obtains a Geass ability that allows her to read the futures of people. She also gains the power to summon a highly advanced Knightmare Frame, using both of these she hopes to find her missing brother.

Nemo
Better known as Magical Device Nemo, Nemo is an entity that gave Nunnally Lamperouge her Geass power, under the terms that she would be Nunnally's knight. Nemo first appears as a mushroom-like doll that was with C.C. in the capsule at the Shinjuku Ghetto. After fusing with Nunnally, Nemo takes on the appearance of an albino Nunnally and is invisible to everyone except for Nunnally. She calls herself Nunnally's reserved anger, the side of Nunnally that is never outwardly shown. When Nunnally activates her Geass, Nemo possesses her body, allowing her the use of her eyes and legs, and piloting the Mark Nemo. Combined with her future-reading Geass, she is now able to easily defeat other Knightmares, but Nunnally's pacifist conscience prevents her from killing all her opponents. Nemo was in fact created from C.C., a fact which she despises and seeks to become whole, not just a clone of C.C.

Alice
Alice is Nunnally's best friend at Ashford Academy. While she may seem like an average girl with some attitude, Alice is in fact a member of the Irregulars, sent to spy on Milly Ashford, and she has a Geass called "The Speed". Nunnally reminds Alice of her crippled sister, which leads her to care about Nunnally deeply, especially when the latter calls her her best friend. Alice discovers from the Ashford's secret files that Nunnally is a former Britannian princess, but decides to delete the file for Nunnally's protection. After an incident with Mao, Alice is determined to capture either Zero, the Mark Nemo and its pilot, or both in order to earn a title of knighthood, in which she can be Nunnally's knight, so she can keep her safe. Alice and Nunnally's relationship is the same of that as Suzaku and Lelouch's, where the two are close friends, but also secretly enemies.

Zero
A masked man who leads the Black Knights against Britannia. In reality, he is Lelouch whose black suit is created from a Geass that grants him immunity. His Geass also allows him to take control Knightmare Frames, and his cape can function as wings for mobility and as a weapon, when in use a Geass symbol appears in his right eye. Lelouch received his Geass from C.C. just as the two were about to be caught in the explosion of the ghettos, which explains how he survived. He takes a more active role in leading his group as now he has brains and brawn, but still maintains Nunnally's safety in mind, albeit being more serious with her. He revealed his identity to Nunnally at Saitama and told her not to get involved, saying he would destroy Britannia for her, and also revealed himself to Suzaku at Narita saying he had powers and asked him to help destroy Britannia.

Irregulars
The antagonists of the manga are the Britannian Special Honorary Foreign Legion "Irregulars" (特殊名誉外人部隊イレギュラーズ, Tokushu Meiyo Gaijinbutai Iregyurāzu?), an elite covert operations unit consisting of non-Britannians who have been granted capabilities far exceeding the human norm by way of ethically questionable medical augmentation. Some members have obtained Geass abilities as a result of cell matter transplants from C.C. The Irregulars unit insignia resembles the bird-like sigil of the Geass, and in combat they pilot the experimental seventh generation series Knightmare Frames called the GX 01 Alpha, which are equipped with a Geass Conduit (ギアス伝導, Giasu Dendō?) system that allows them to channel their abilities into their Knightmares.

Dalque
Dalque (ダルク, Daruku) is a dark-skinned girl who serves as point man for the Irregulars. She possesses a Geass ability known as "The Power," which augments her physical strength by exaggerating the magnitude of macroscopic forces. When her ability is active, a Geass sigil appears upon her forehead. Her Knightmare Frame cockpit is installed with synchronization receptors that allow expression of this ability as a highly effective frame strength enhancer.

Lucretia
Lucretia (ルクレティア, Rukuretia) is a pale-haired girl who is a member of the Irregulars. She possesses a Geass ability known as "The Land," which accurately maps three-dimensional terrain within a given range. The results of her perceptions are instantly submitted to her Knightmare Frame via a cockpit neuro-imaging device and collated with GPS data before being distributed to her team for tactical purposes. When her ability is active, a Geass sigil appears upon her forehead. She is typically partnered with Sancia, whose tracking Geass ability complements her own. Of the three, she is the calmest of them all and regards her team as siblings as she had lost all her relatives in the war.

Madd
Madd (マッド, Maddo) is an unpleasant male cyborg who serves as the Commander of the Irregulars.

Sancia
Sancia (サンチア, Sanchia) is a dark-haired woman who serves as a field captain for the Irregulars. She possesses a Geass ability known as "The Order," which accurately identifies the positions of targets within a given range and precisely calculates their probable movement trajectories based on all known variables. The results of her calculations are instantly submitted to her Knighmare Frame via a cockpit neuro-imaging device and collated with radar information before being distributed to her team for tactical purposes. When her ability is active, a Geass sigil appears upon her forehead. She is typically partnered with Lucretia, whose terrain-mapping Geass ability complements her own. She is older than her subordinates.

Suzaku Kururugi
Lelouch's best friend and Euphemia li Britannia's knight. Suzaku first met Lelouch and Nunnally when they were forced to stay at the Kururugi Shrine in Japan, although the two hated each other at first, Nunnally helped facilitate peace between the two. When Britannia invaded Japan, Suzaku's father tried to kill Nunnally but was stopped by C.C., after that the Britannian siblings were returned to their homeland and were pronounced dead, though Suzaku felt this was a lie. He joined the Britannian military, became a part of Lloyd Asplund's team, and eventually became Euphemia's knight through Schneizel's approval. He occasionally visits Nunnally at Ashford though is not enrolled as a student, and usually calms her down about whatever it is that bothers her. He still pilots the Lancelot like in the anime, though its design is slightly different and it is equipped with the same Geass Conduit Systems as the Knightmares of the Irregulars. In addition Suzaku is revealed by Zero to be a 'Wired' a being who can access the power of Eden Vital without entering into a Geass Contract and thus having the qualifications to become a 'Demon King' the same as Zero.

Rolo vi Britannia
Lelouch's twin brother that looks like Lelouch himself. Rolo had been taken from Marianne when he was a baby, due to the superstition of twin princes bringing misfortune. Therefore, his existence is unknown to Lelouch and Nunnally. He is involved with the Geass Order and known as The Cardinal. He pilots his very own customized Vincent Knightmare Frame and his piloting skills are somewhat ruthless and cold. He first appeared in chapter 10 with Schneizel, who is heading to Area 11, and later meets Suzaku, who can tell that he's not Lelouch. Like Nunnally and Lelouch, Rolo has access to Geass powers, and is able to summon his own personal Vincent Knightmare Frame. His Geass, "The Ice", possesses the same ability as the original Rolo's (to halt one's experience of time) and as the name implies, encases its victims in a layer of ice. He plans to kill Nunnally and Lelouch so that he can take their powers to become the true Demon King and overthrow the Emperor.

In reality, he is not Lelouch's twin at all, but rather a clone created from the DNA of Charles and Marianne, and then brainwashed into believing he was the twin brother of Lelouch.

Chapter 1: The White Witch and the Black Demon Awaken
After Lelouch disappears amidst the destruction of the Shinjuku ghetto, Nunnally attempts to find him, but instead she finds an entity called Nemo who gives her the Geass ability. Summoning a Knightmare, she defeats the Britannian military, but spares Clovis after realizing that it is not what Lelouch would have wanted. Elsewhere, Madd, a cybernetic man, observes the battle and transfers the information on to a dark-haired woman, Sancia, who tells him that the maneuvers performed are impossible for a standard Knightmare frame, and that the presence she felt from its pilot was not human. Madd asks if it was C.C. or Nemo, as both of them depend on their host, but Sancia does not know, only replying that the pilot was a Geass user.

Madd, excited from the news, orders all members of their group to report to Area 11 once they are done with their mission in Area 5. Curious about a Knightmare that runs on the heresy of something called the Eden's Vital, he asks another member in the shadows, "Wouldn't it be an adequate opponent for the Irregulars?". The member, wearing a uniform with a Geass symbol, does not reply.

At a government complex, Clovis is told to sign a report for the Shinjuku incident, but he refuses out of embarrassment. A shadowy figure appears, stating, "If the Emperor finds out about the Shinjuku massacre, the C.C. project being exposed, and the defeat of 18 Knightmare Frames, you might be disowned." A shocked Clovis tries to call for help, but the figure has shut down the electronic system. The figure tells Clovis that he will suffer the same fate as the residents of Shinjuku. Terrified, Clovis attempts to gun the man down, but the bullets have no effect. The man then pulls out a gun and reveals himself as Zero, the one who will destroy Britannia.

Chapter 2 and Chapter 3: Nemo and the Irregulars
Cornelia li Britannia and her knight Andreas Darlton are surprised by the events taking place in Area 11. Cornelia asks the status to which Darlton replies that Clovis's body has been taken in for an autopsy and that the crime seen has not been touched as she requested. Cornelia satires at the blood writing on the wall and asks what it means, her other knight Gilbert G.P. Guilford translates it into "to smite evil in heavens name". Cornelia orders for all information regarding Clovis's death to be withheld from the public, she deduces by the words on the wall, and what the security cameras caught on tape that Britannia is being challenged, she also orders the mysterious masked man to be brought to her. At Ashford, Milly Ashford informs Nunnally that there is still no word from Lelouch, and that it will be almost impossible to obtain a search warrant to find him. She tells Nunnally that she has told the student body that he has enrolled in an exchange program and has returned home, but reassures her that they will find Lelouch. Nunnally thanks her for all that Milly and the Ashford family has done for them, once alone she is told by Nemo that "their" brother is not dead, but that she is also unsure if he is alive. A confused Nunnally asks what she means, who she is, why even though she is blind why she can see her, and why she looks like her. Nemo responds that it is because of the contract, she reminds Nunnally that she wanted power, so for that she gave her a Knightmare Frame and a Geass that allows her to read the future, but in return she took something from Nunnally. When asked what, Nemo says that she took the darkness in Nunnally's heart, emotions born from that darkness such as anger, sadness, and vengeance she used to evolve from a mud doll to a higher state of being. Nunnally begins to ask more, but Sayoko Shinozaki, her maid, enters and asks who she is talking to. She leaves Nunally breakfast and leaves, Nemo then explains that she was created from the cells of a witch and that only Nunnally can see her. She reveals herself as Magical Device Nemo and says she is the other Nunnally and following their brother's wishes she has become Nunnally's protector, she finishes up by telling Nunnally to eat or they will be late for school. As she leaves three other students begin to bully her, but Nunnally just ignores them, causing the leader to knock her out of her wheelchair. Nemo prepares to interfere but out of nowhere another student appears in the blink of an eye, she tells them that they are just bullies and shows that she has stolen their skirts. They run off and she helps Nunnally up and she is revealed to be Alice, Nunnally's friend, Nunnally thanks her and Alice takes her to class. Elsewhere the Japanese resistance meets with their ally from the Shinjuku Ghetto, who turns out to be Zero, and explains that they have the same goal, the annihilation of Britannia. Alice and Nunnally chat about how Alice has stood up for Nunnally ever since the first day they met, Alice explains that she has a younger sister that is also in a wheel chair so Nunnally reminds her of her. Alice apologizes if Nunnally does not like it when she feels bad for her, but Nunnally corrects her saying the reason she comes to school is because of her best friend, Alice. Alice assures her that her brother will come back soon from his studies and since her best friend is here, she should cheer up. Nunnally thanks her, they return home and Nunnally invites her in, but Alice says she has something to take care of, so they say goodbye and Alice recalls what Nunnally said about her being her best friend. In Area 5 a sub Britannia military group is being wiped out by three Knightmares bearing the Geass symbol. Two of the pilots themselves use unusual Geass powers called "the Odd" and "the Land" to locate the remainder of the Britannia group, the third one finish them off using a Geass called "the Power" to lift a building and flatten them. With that done, the leader, Sancia, announces that it's time for their next mission. Another member, Lucretia, asks where their next mission is, Sancia says it is in Area 11, the third member, Dalque, asks whats the target, Sancia replies it is a Geass user.

Chapter 4, Chapter 5 and Chapter 6: Incident at Lake Kawaguchi
Deciding a trip would help lighten the atmosphere, Milly organizes a trip to Lake Kawaguchi for the entire student council. However they along with the other guests are soon taken hostage by the Japanese Liberation Front, and Nunnally is brought in for questioning by the leader, who recognizes her as the a princess of Britannia. When Japanese terrorists sees Nunnally friend Alice they shot her point-blank and she falls out of the tower, her rage causing her to summon the Mark Nemo and fight back. However, Alice survives the shot with the power of her Geass and races back to the hotel in her own Knightmare Frame to rescue Nunnally, only to find herself facing the Mark Nemo. She jumps to the conclusion that the Mark Nemo is an enemy and starts fighting it, but their fight is interrupted when Zero appears and reveals the Order of the Black Knights to the world. Alice manages to escape and regroups with the irregulars who came to help, revealing that is she is also a member. Piloting a unique human shaped Knightmare Frame exclusive to the Irregulars, the Alpha, she goes in alone to rescue Nunnally. Nemo summons the Mark Nemo, when the leader threatens Alice's life, but before she can kill him, Nunnally, with encouragement from Lelouch in her mind, finally makes Nemo submit to her will, and they leave to save Alice. The two friends encounter one another, and not knowing it is them believe that the other has hurt the other, resulting in a duel. The pair are evenly matched; Alice's Geass, The Speed, gives her blinding speed, which allows her dodge Nunally's attacks and Nunnally is able to avoid being hit thanks to her future reading Geass. The fighting is brought to an end when the building collapses, but the hostages are saved, the ones who saved them are revealed to be Zero and his new Order of the Black Nights. Zero introduces them as heroes who protect those without power from those who have it, and declares war on Britannia.

Chapter 7: The White Knight
In the aftermath of the Lake Kawaguchi incident, Zero and the Black Knights begin getting much recognition. Kyoto questions whether Kaguya Sumeragi should give the Black Knights Burai Knightmare Frames as well as the Guren MK-II, but she reassures them that it is alright. Back at Ashford, Nunnally has a nightmare about Alice's death, but Alice is able to calm her down. Madd meets with Lloyd Asplund, who finds the Alpha impressive. Madd is surprised to find Lloyd and his team in Area 11, but Lloyd says it should be obvious as Princess Euphemia li Britannia is there as well and her knight is their test pilot. He also requests information on the Mark Nemo, but Madd says all they know is that its an unknown Knightmare Frame, but tells Loyd they will send more data later. Content, Lloyd leaves, but not before telling Madd his team has also completed a seventh generation Knightmare with a muscle framing system and same features as the Alpha, angering Madd. At the government building, Euphemia's knight, Suzaku Kururugi, gives his report to Princess Cornelia li Britannia, he also tries to talk about the scheduling for his meeting with Euphemia, but Cornelia remarks that she has a much worse schedule as she is the Governor. On the way out, Cecile Croomy acknowledges that she knew Cornelia would be cold towards him, Suzaku comments on how the only way he became Euphemia's knight was because he had Schneizel's approval, and that Cornelia more than likely hates the idea that an Eleven is her little sister's protector. Cecile is still surprised that even though he is her knight that Cornelia would still deny him an audience with Euphemia, but Andreas Darlton appears and comments that Cornelia draws the line between Nobles and numbers, and that he too does not approve of Suzaku's knighthood, and challenges him to a duel, to see if he deserves it. In the Ashford Academy basements, Alice discovers from the servers that Nunnally is a former princess of Britannia, and her mother the late Marianne vi Britannia.Knowing it's her mission to report anything the Ashfords might be hiding, she instead decides to delete the file as Nunnally "Lamperouge" is her only friend. Suzaku, piloting the prototype moble suit Z-01 Lancelot, begins his duel against Darlton, who's more than confident he will win. Lloyd, who's finished greeting Clovis's stand alone unit, also watches the duel. Darlton attacks but Suzaku easily outmaneuvers him, angering Darlton and asks why Suzaku hasn't drawn his sword. Suzaku answers that there is only arrogance and greed in Darlton's weapon, the two things that do not recognize him, an eleven, as a knight, and that which insults him, for that reason Suzaku does not see it as a duel between knights and that is why he will not draw his sword. Darlton accuse him of wimping out, but Suzaku retorts that since he is Euphemia's knight, he will fight to uphold her honor, but still refuses to draw his weapon against Darlton's tainted one. An enraged Darlton lunges at him, ready to kill, however the duel is stopped by none other than Euphemia, reprimanding the two for their actions.

Chapter 8, Chapter 9 and Chapter 10: The Disaster at Saitama
Alice discovers Nunnally's true identity as a Britannian princess, but declines revealing her identity to her superiors, believing that her friendship with Nunnally is more important. Suzaku also makes an appearance as he joins the Britannian military and is chosen to be Princess Euphemia's knight. Suzaku decides to pay Nunnally a visit, but the Princess decides to stay outside, saying she doesn't want her to get dragged back into Britannian politics. Afterwards, the Empire tries to spring a trap at Saitama in order to wipe out the Black Knights. Nemo coaxes Nunnally into joining the battle, saying that the alternative is to watch as hundreds of people die. As the Japanese resistance forces suffer many casualties, Zero springs a counterattack, taking on a few Knightmare Frames by himself and disabling them with some strange handheld device while the Black Knights provide support. As Nemo joins in the battle, the Irregulars spring a trap of their own, using a Gefjun Disturber to paralyze the Mark Nemo. The Irregulars prepare to snipe the cockpit of the downed Mark Nemo so that they can collect the DNA of the dead pilot, while Cornelia comes face to face with Zero and prepares to take her own life before giving Zero the satisfaction of victory. However, Suzaku appears in the new Lancelot model, saving Cornelia from Zero while the Mark Nemo breaks free of her own constraints and manages to block the sniper shot.

Eventually, the Black Knights inflict enough damage that the Britannian forces are forced to withdraw from the area. Alice is angry because she wanted to finish off the Mark Nemo once and for all, but doesn't get the chance.After the battle, C.C. reveals that she was wearing the suit of Zero the whole time, and confronts Nemo alone as Nunnally lies unconscious from the day's events. Nemo claims that she was actually derived from an aspect of C.C., yet has her own agenda now that she has been feeding off the anger and strong emotions of Nunnally. She claims she wants to be free from "this mud puppet" and will do whatever it takes to get her own identity, while C.C. chides her. Near the end of the story, after Prince Schniezel has a talk with Princess Cornelia, he exchanges words with another young man who appears to be Lelouch vi Britannia.

Chapter 11, Chapter 12 and Chapter 13: Prison of Happiness
Both the Black Knights and The Irregulars have word of some drug called "Refrain" that is spreading around the Japanese population, a drug that traps people within their past memories and continuously loops them until they suffer permanent brain damage. The Irregulars believe that it could be connected to Mao, "The Refrain," a Geass-user who deserted the unit some time ago. Back at school, Nunnally has a chat with Nemo, who tells her that C.C. is actually a copy of Joan of Arc (or perhaps even the original) who survived the Hundred Years War because she is an immortal witch. That same witch apparently entered a contract with Lelouch, who asked her to protect Nunnally. While Nunnally mulls over this, Mao appears behind her, and unwraps bandages on her own right arm. She reveals that the Geass is slowly eating away at her body, even though injecting herself with C.C. cells helps temporarily she will die without help. Apparently, Mao's Geass allows her to read minds. Just as the Mark Nemo is about to appear to fight her, Mao opens up her left eye and plans to trap Nunnally in a "Prison of Happiness." While under this effect, Nunnally recalls a childhood experience of her first meeting with Suzaku and time spent in the Kururugi household, and how C.C. was involved directly or indirectly with all of them.. While she is reliving her memory, Suzaku is simultaneously telling Euphemia the same story.

Mao tries to absorb Nemo's power, but the entity somehow turns into Lelouch, and then C.C. herself, and rejects Mao. Finally, Alice shows up with a gun and a briefcase containing C.C. cells. Mao pleads with her for the drug, but Alice's speed is too much for Mao to handle. Then, in an act of cruelty, Alice simply shoots the drugs with her gun and watches Mao crumble into dust. As Mao slowly withers away, she tells Alice that this will be the fate of all Irregulars. Alice retrieves the unconcious Nunnally and vows to protect her.

Meanwhile, a hooded figure reports Mao's death to the character resembling Lelouch vi Britannia.

Chapter 14, Chapter 15 and Chapter 16: The Battle at Narita
When Suzaku meets Alice during his second visit to Nunnally, he offers a friendly handshake to her; but when the two hands come into contact, Alice gets a strange feeling and retreats, puzzling both Suzaku and Nunnally. Alice later remarks that the feeling is the same as when she came into contact with Zero back at Saitama, leaving her to wonder what Suzaku is. After Suzaku leaves, Nemo reveals to Nunnally that, through reading Suzaku’s future lines, learns that the next Britannian operations will take place at Narita, the Japan Liberation Front’s headquarters.

At Narita, the Japan Liberation Front is easily annihilated by the Britannian Army, despite putting up a good fight. However, it is soon revealed that the operation is an ambush set up by the Black Knights, who immediately cause an avalanche that wipes out most of the Britannian forces, isolating Cornelia who is confronted by Zero again. As Cornelia prepares to let herself be killed rather than captured, Suzaku, piloting the Lancelot, arrives and rescues her on behalf of Euphemia. After Cornelia reluctantly retreats, Suzaku engages Zero in combat. Zero tells Suzaku that he(Suzaku) is a Wired and shows him what his powers meant by showing him the history of C.C. In the flashback, Suzaku first witnesses C.C. fighting Jeanne D’Arc (who is portrayed as evil in this version), the Witch of Orleans during the Hundred Years War and afterwards betrayed by the country she served by being burned at the Stake on false charges of witchcraft. However, C.C. survived due to being cursed by Jeanne prior to the latter’s execution, which allows her to live on for eternity. Having been betrayed by the world she previously held dear, C.C. renounces her humanity and becomes the new Witch, determined to become the Demon King. The flashback then changes to a scene where Marianne, prior to her assassination, entrusts the lives of her children, Lelouch and Nunnally, to C.C., hence the reason why C.C. killed Genbu Kururugi, as he tried to kill the two children in an act of desperation to end the War on Japan. Finally, Suzaku witnesses Lelouch’s encounter with C.C. at the Ghetto, in which Lelouch accepts a contract with her, gaining the powers to become a Demon King.

When the flashback ends, Zero takes off his mask, revealing himself as Lelouch! Lelouch explains to a surprised Suzaku that his (Suzaku) being a Wired possesses the power to become a Demon King and offers Suzaku a chance to join him so they can create the “kind and gentle” world that Nunnally wished for. However, Suzaku furiously claims that the Lelouch in front of him is an illusion created by the Witch and attacks him, easily defeating him. As Suzaku prepares to arrest the defeated Zero, Mark Nemo arrives and engages Suzaku in battle, but they are soon interrupted by Alice piloting her Knightmare Frame, who is determined to defeat Zero and Mark Nemo in order to obtain a knighthood and protect Nunnally. Alice easily overpowers Mark Nemo, but the battle is soon interrupted by an unknown Knightmare Frame which fires energy particles towards the ground, scattering the combatants. As the smoke clears, Alice crawls out of her wrecked Knightmare Frame, revealing herself to Nunnally and Nemo. Nemo claims that Alice has revealed herself to be a traitor to them and urges Nunnally to kill her, but Nunnally refuses, and her refusal to give in to her anger results in her contract with Nemo being cancelled, causing Nemo to revert to her original doll form and the Mark Nemo to be dissolved, revealing an unconscious Nunnally to a shocked Alice.

Chapter 17, Chapter 18 and Chapter 19: The Genealogy of Witch
The story opens with a flashback depicting Nunnally and Alice’s first meeting and the start of their friendship. It then fast forwards to the present where Nunnally is revealed to have been captured and imprisoned by the Britannian Government. Alice, while trying to prove Nunnally’s innocence, learns that Nunnally has been handed over to the Heretical Trial Division of the Eden Vital Religious Order, where she will most likely be executed, despite her royalty status. As Alice confronts the Cardinal of the Eden Vital Order (who strongly resembles Lelouch), he easily knocks her out and places her under arrest. The Cardinal then visits Nunnally in her cell and reveals himself as Rolo vi Britannia, the unknown twin brother of Lelouch. Rolo explains that, being one of the ‘twin princes’ and considered a curse, he was forced to live an unknown existence until the ‘deaths’ of Lelouch and Nunnally at Japan allowed him to reclaim his royal status and his current position as Cardinal. He declares that his purpose is to deliver death on both Nunnally and Lelouch.

In the meantime, Suzaku learns of Rolo’s identity through a file obtained by Euphemia, and later encounters Lelouch, who reveals Nunnally as the pilot of the Mark Nemo and asks for his help to save her. Suzaku immediately passes the information to Euphemia, who contacts her sister to plead for her help to save Nunnally, their half-sister and the daughter of the late Marianne, whom they both held a deep respect to. However, Cornelia is reluctant to act due to the Cardinal’s authority surpassing her own, and Euphemia decides to take matters into her own hands: Interrupting the execution, Suzaku, following Euphemia’s orders, pilots the Lancelot to save Nunnally, but finds himself locked in combat with Anya Alstreim, Rolo’s knight. Lelouch, in his Zero disguise, uses the opportunity to retrieve Nunnally, but he also finds himself blocked by Rolo, who reveals his own Knightmare Frame and engages battle with him.

While the battle is happening, Nemo approaches Alice in her prison cell and explains to her Nunnally’s Geass and powers. She asks Alice to form a deal (not a contract) with her if they are to save Nunnally. Alice is initially hesitant out of fear for repeating the same mistake she made on failing to protect her little sister, but with convincing from Nemo, Alice finally agrees to the deal and gains new abilities as a result. She then breaks out of her cell and reaches the execution site just as Suzaku and Zero are being defeated by their Eden Vital opponents. Alice reveals her newly-gained abilities in the form of a new Knightmare Frame called “Code Geass.” Unleashing its powers, Alice causes a huge explosion of light that wipes out a large part of the government facility building (but not killing anyone). When the light has cleared, Alice, Nunnally, as well as Zero, have vanished. Angered at this, Rolo shouts out “CODE GEASS! KNIGHTMARE OF NUNNALLY!”

Chapter 20, Chapter 21 and Chapter 22: Demon King Rolo
Following the escape, Cornelia and Euphemia hold an emergency meeting with Rolo to question his role on the destruction of the government facility building. However, at the moment the clock stroke midnight, Rolo has the Governor Generals arrested, acting on an order from Emperor Charles in which the Governor Generals of all the areas are to be arrested on charges of treason and their positions replaced by the Cardinals of the Eden Vital Order. When Schneizel el Britannia, as Imperial Prime Minister, informs Charles that the Imperial Senate had moved to veto Charles’ order, the Emperor responds by dissolving the Senate and placing all its members, including Schneizel, under arrest. Charles then declares that the Holy Britannia Empire shall be re-organized into the “Holy Nation of Eden Vital.” Cornelia and Euphemia, along with all their subordinates (including Suzaku, Guilford, Lloyd and Cecile) are put into prison, but they are later broken out by the combined forces of the Black Knights and the House of Kyoto, with the latter’s leader, Princess Kaguya, offering a negotiation with them.

After bringing Nunnally to a secret hideout, Alice notices a geass reaction on Nunnally’s arm. Knowing that Nunnally would end up like Mao, Alice figures out one possible solution – Rolo. In the meantime, Rolo enlists the Irregulars to help him hunt down Alice, but as they near the hideout, the Irregulars reveal that they have lured Rolo into a trap, out of loyalty for their friend Alice. However, Rolo reveals his Wired Geass – The Ice, which freezes time, and overpowers the Irregulars. Alice arrives in time to prevent Rolo from destroying her friends and a battle commences between the two of them. Both Alice and Rolo are equally challenged with their geass powers, but Rolo soon reveals the captured Nunnally, whom he managed to obtain by using the Irregulars as a decoy. Believing that he has gained the upper hand, Rolo prepares to kill Nunnally, but Alice reveals the ultimate technique of her geass – The Code Geass Godspeed, and uses it to destroy Rolo’s Vincent Knightmare. After being beaten, Rolo notices a geass reaction on his arm and realizes the truth of his birth – An artificial clone created using Charles and Marianne’s DNA and injected with C.C. cells, and then brainwashed into believing he was the Demon King. Afterwards, Rolo crumbles into dust in Anya’s arms. Anya tells Alice that the answers to all her questions lie on Kaminejima and tosses her a locket before departing. Both Alice and Nunnally later discover that the locket contains a family photo of Nunnally with her family – her mother and brother.

Chapter 23, Chapter 24 and Chapter 25: Island of God
Following the prison breakout, the leaders of the Six Houses of Kyoto - Taizō Kirihara and Princess Kaguya, hold a meeting with Cornelia and Euphemia, in which they reveal that following Charles’ proclamation, chaos have occurred in several areas yet the Emperor has taken little action about it. Therefore, the only possible solution to counter this would be to crown a new ruler, which they nominate Euphemia, as she had been negotiating with Kyoto about Japanese temporary autonomy. When Cornelia mentions the legal conditions to do so, which requires at least 80% of Senate approval and half of Royalty approval, Taizō reveals a secret file that had been sent to them by Schneizel, in which he and the entire Senate had approved of Euphemia’s crowning, as well as the knowledge that Cornelia is the only royal member left that can legally approve of her sister. Euphemia is hesitant at first, but with Kaguya’s encouragement, she ascends to the throne as the 99th Empress of the Holy Britannian Empire. In her inauguration speech, Euphemia renounces the Pax Brittanian policies and declares the birth of a new Britannian Empire, along with the liberation of all the areas. Simultaneously, Zero announces to the Black Knights that they will seek an alliance with Euphemia’s Britannian Empire and together, they will bring down their common enemy – Charles the Absolute. After learning that Charles is at Kaminejima, the combined forces of Britannia and the Black Knights set off there and launch their first strike on Charles’ forces, only to see them recover from the blows apparently unharmed. Zero explains to Suzaku that these zombie-like fighters are Charles’s elite forces - the Knights of Rounds, and they are now fighting against immortals. The fight against the Knights of Round soon prove to be difficult, with the Knights easily defeating the Knightmare Frames until only Zero and Suzaku’s units are left standing. However, Zero tells Suzaku that they have to hold their ground while Nunnally is dealing with the Emperor.

Meanwhile, Alice and Nunnally also arrive at Kaminejima on the Code Geass Knightmare Frame. They enter a mysterious dimension where Nunnally meets with her father as well as her mother, who is revealed to have been alive due to transferring her soul into Anya, the assassin originally sent to kill her by her political rivals, through her Geass, and has been posing as Anya since then. Charles and Marianne explain to their daughter of their early beginnings as idealistic youths who had dreams for a peaceful world, only to have them shattered when they were assassinated by political rivals. However, through their deaths, they were able to be reborn due to their newly-acquired Geass powers and use them to bring the whole world under their control. They also reveal that Nunnally’s ability to see the lines of the future was merely a side-effect of her true Geass: "The Zero." Nunnally's Geass allows her the ability to interact with C’s World to open Heaven's Door in order for all people to become one, which her parents claim will bring true peace and happiness to the world. Nunnally approaches Heaven’s Door, but after hearing Alice explain on what she (Nunnally) means to her (Alice), she refuses to carry out her parents’ plan, stating that there is no future in the plan that her parents want, and that she chooses to accept herself, regaining her sight and mobility in the process. This causes Heaven’s Door to collapse, as well as Charles, Marianne and Mark Nemo to disappear forever, which they accept as their daughter’s choice. Charles’ defeat also causes the Knights of Round to disappear as well, bringing the battle to a victory for Britannia and the Black Knights.

As Alice and Nunnally emerge from C’s World, Alice tells Nunnally that she is willing to believe in the future of the world she chose, and Nunnally thanks Alice for it.

Chapter 26: Zero of the Demon King
Following the defeat of Charles the Absolute, Euphemia officially succeeds him as Empress of Britannia. Although she upheld her vow and liberated all the Areas, it turned out to be a completely difficult task, as the transferring of power had to be handled gradually, during which public order had to be handled by both the Britannian Forces and the former Rebel forces. However, skirmishes still occurred between them, and with the world having lost Charles as its enemy, once again focused their hatred towards Britannia, proving a new challenge for Euphemia. Thus, the world was thrown into chaos once more.

It was also announced that Zero had perished at the Battle of Kaminejima, however, on the day of Euphemia’s official crowning and the signing of the peace treaty with Japan, Lelouch appeared in front of Suzaku and Euphemia to bid them farewell as it is his last day as Lelouch. He then meets with Nunnally, who is now a goodwill ambassador of Japan, and discusses about their Geass. Lelouch explains that from Nunnally's Geass, "The Zero", he had been freed from C.C.'s duties by death, as her soul had now returned to Eden Vital and he has been made as her successor like many others before her and all the Geass that she bestowed upon have now disappeared. When Lelouch asks Nunnally’s reason for not opening Heaven’s Door, Nunnally explains that when she came into contact with it, she saw countless alternate realities, one of which is the “Lelouch of the Rebellion” anime. Through this, Nunnally realizes that their world was just one of many universe possibilities, and that Eden Vital is only of the past, but as long as there’s a future for humanity, then the ideal for the peaceful world will definitely be achieved. Lelouch remains upset that she did not accept their parents’ plan, but acknowledges her dream for a peaceful world, to which he gave her a hug and bids farewell before saying that her brother will still love her. As Lelouch leaves, he asks his sister to help someone else who is also lost like him.

At Ashford Academy, which is now operating as a refugee camp, Alice and her now ex-Irregular friends are shown working there for a living following the loss of their Geass and the disbandment of their military unit. When Alice gets the rest of the day off after work, she goes to the rooftop where she meets with Nunnally. Alice explains that she left Nunnally shortly after their rescue because she realized that although she helped Nunnally make the right decision of not destroying the world, it was still, in Alice’s view, not a peaceful world for Nunnally, as it was one where all those dear to her – her mother, father and brother no longer existed, as well as Nunnally being a target of the world’s hatred due to her role as Britannia’s ambassador to Japan, and Alice feels that she had failed as Nunnally’s Knight because it would be a painful experience to Nunnally. However, Nunnally explains that no matter how painful the experience is, the world still has a future with hope. She then presents Alice a knight’s emblem, asking Alice to be beside her if she still believes in the future she chose. This time, Alice accepts.

At the series’ conclusion, Lelouch gives a monologue about Eden Vital and Geass, before emerging as C.C. the Demon King, and goes forth to spread Geass and to promote conflict around the world.

Differences from Lelouch of the Rebellion
One of the main differences in Nightmare of Nunnally is in the type of Geass that are shown. In the original series, Geass typically only affects the minds of others - with the exception of the Geass of the Knight of One, who can partially see into the future. However, in this series Geass is not limited to the mind. An example of one such Geass is Alice's Geass which gives her blinding speed.

Lelouch also receives a different Geass ability than in the anime. In this version, instead of gaining the power to make others obey his commands, he gains a suit of black armor with multiple capabilities, the foremost of which is immunity from attacks and the ability to hack into and take control of Knightmare Frames.

The manga follows some of the same basic events as the original story line, but in a different sequence. In the anime, the Lake Kawaguchi hostage crisis comes after the Saitama disaster, but in this version, Lake Kawaguchi happens soon after Nunnally meets Nemo and then the story goes into the confrontation with Mao.

While both Rolo and Mao appear in this manga, they appear as completely different characters from their anime counterparts. Mao appears as a young girl previously aligned with the Irregulars, while Rolo appears as Lelouch's twin bother that looks alike, separated at birth, but still affiliated with the Geass Order.

Charles and Marriane are also more understanding, like when Marianne doesn't protest against Nunnally's decision to go against their plan, and Charles only rages for a bit, unlike his anime counterpart where he keeps yelling.

Another significant alteration to the plot is Euphemia's fate. Since Lelouch has a different Geass, he could not command her to "kill all the Japanese", so he is not forced to kill her. Indeed, she ultimately becomes the 99th Empress of Britannia rather than Lelouch. However, the ending can be considered bittersweet - on the one hand, Britannia once again becomes the target of the world's ire after Charles' defeat even after she frees all of the Areas; on the other, Suzaku gets to continue serving as Euphemia's Knight, indicating that they'll find happiness together.