When Japanese terrorists appear at Kawaguchiko, Nunnally sees her friend Alice get shot point-blank and fall 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.
Later at Ashford Academy, Nunnally wakes up in a bed with Alice at her bedside, neither of them realizing that they fought each other in Knightmare Frames. 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.
Afterwords, 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 Gefion 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.