Skirmish in Shinjuku Ghetto

The Shinjuku Ghetto Skirmish began after Prince Clovis La Britannia ordering the destruction of the Shinjuku Ghetto in order to retrieve C.C. from an un-named resitance cell using the ghetto as cover.

Two Area 11 terrorists, commandeering a military truck they beleived contained poison gas, containing the secret military experiment designated “C.C.”. The subject was contained inside a large steel sphere. Initially, the police pursuing the terrorists were told only that a container filled with poison gas was stolen. As soon as Prince Clovis was informed of the gas's theft, he ordered the army and Knightmare Frames to apprehend the terrorists and retrieve the canister. Before the army mobilized, bystanders reported that the truck swerved off a highway, hitting a nearby building. Lelouch Vi Britannia climbed into the back of the truck to investigate and help if possible. The truck, its driver regaining consciousness, drove off again. The army engaged the terrorists back on the highway, and one of the fighters launched a Glasgow-class Knightmare Frame from the truck. While one Britannian Frame diverted the truck into the subways of the Shinjuku ghetto, a soldier in a Sutherland-class Frame partially disabled the Glasgow; however, both truck and Frame were lost in the subways. Private Suzaku Kururugi spotted the truck and then reported a Britannian student first. When his unit caught up to him, C.C. had been freed from its container. Shocked, Suzaku was ordered to kill the stowaway student. When he refused, his commanding officer shot him. Almost immediately, the truck exploded, self-destructed by the driver; the student and C.C. were lost in the following confusion.

Shortly afterwards Prince Clovis ordered the destruction of the Shinjuku ghetto in order to find the test subject. When an Britannian commander, locating Lelouch by the sound of his cell phone, ordered that both be killed, C.C. jumped in front of Lelouch and was shot in the head. The commander, after boasting he would blame her death on the terrorists, ordered all his soldiers to prepare to fire. However in a spilt second C.C. grabbed Lelouch's hand and formed a contract for Geass. Lelouch immediately used his geass and ordered the soldiers of the unit to committed suicide.

Villetta Nu, scouting for the stolen capsule, reported that she had seen a student in an abandoned warehouse. Lelouch used his new found power and ordered her to exit the frame. Here, he found out that his Geass doesn't doesn't work unless direct eye contact can be sustained. Villeta Nu went out of the frame to confirm his identity. The moment she exited her frame, Lelouch used his geass and ordered her to hand over her Sutherland. She blacked out and upon awakening, both the student and her knightmre frame were gone.

Jeremiah and his group were still chasing the partially disabled Glasgow that Kallen is piloting. She is contacted by Lelouch and listens to his orders by leaping onto a military train to evade capture. As Jeremiah slowed down the train, he orders another unit to chase after the Glasgow. However, Lelouch who is piloting a Sutherland is able to help Kallen destroy their pursuers' knightmares. Lelouch, then contacts Ohgi's group and asked that they follow his orders. His order was for The other terrorists to regroup at the train, which contained 11 Sutherland-class Knightmare Frames. The rebels stole all 11 Frames and began systematically destroying all Britannian units in the area, with help from the Glasgow under Lelouch's orders. Prince Clovis gave the order for all units to surround the area where the rebels were suspected believing victory in numbers, but the rebels—having retreated to the subways—collapsed the ground underneath the units, effectively destroying them.

Prince Clovis then authorized the use of the new Lancelot, the first seventh-generation Knightmare Frame. Piloted by Suzaku, the Lancelot quickly took out all eleven rebel Frames without any damage; the pilot also spotted the stolen Sutherland Frame hiding in an abandoned skyscraper, and engaged it in battle. The Sutherland pilot destroyed nearby buildings in hope of blocking the Lancelot. The Lancelot’s pilot stopped to rescue an Area 11 civilian from the debris, resulting in the loss of the terrorist. Shortly after, a group of soldiers found Area 11 civilians and suspected terrorists hiding in an abandoned warehouse. Lelouch, who had escaped, immediately went to Clovis's G-1 Base vehicle disguised as a Britannian soldier. He made his way inside to where Clovis was seated happily enjoying his near victory. Lelouch, surprising his half-brother by removing his mask, holds Clovis at gunpoint and orders him to give a ceasefire, promising to spare his life in return. At this point the Britannian Task Force had located the hiding place of the terrorist group, mixed in with civilians. Before the criminals could be captured or executed, Prince Clovis gave his order for a ceasefire.

Lelouch decides to kill his brother despite his cooperation, reasoning that Clovis would change nothing.

Aftermath
With Prince Clovis’ assassination, Margrave Jeremiah Gottwald took temporary command of Area 11. He captured the rogue Britannian officer Bartley Asprius in the midst of moving his secret, unauthorized laboratory from Tokyo to Narita. When captured, Asprius admitted he was the one experimenting with the test subject Clovis and that the canister had never contained poison gas. Asprius was stripped of his rank and sent back to Britannia. An investigation could find evidence pointing to any identifiable suspect, so officer Kururugi was held responsible for Prince Clovis’ assassination, being both a easy scapegoat and one of the few soldiers who would have something to gain.