Got a bad reception on the Naruto board, but here's a repost of a [Code Geass / Naruto] fusion I came up with a while ago. Note that despite not being in the role of Lelouch, Naruto is the main character:
So, a scenario:
Orochimaru betrays Konoha significantly earlier than in canon, kidnapping Uchiha Mikoto (who was bethrothed to Fugaku in a marriage between cousins) for assorted purposes and killing the rest of the Uchiha family. He establishes a hidden village in the minor nation of Fields and adopts a philosophy of meritocracy and extreme efficiency. Not so subtly, he pushes the country toward rapid expansionism.
After a some years, he manages to conquer and take control of the majority of the states within the surrounding region, establishing what is dubbed "the Empire of the Sound." Uchiha Mikoto has been brainwashed into becoming one of his concubines, and is now also a trusted military leader on the battlefield, nicknamed "Oto no Kuroi Senkou" -- she has full control of her Sharingan, despite never having demonstratied significant talent with it as a chuunin in Konoha. By Orochimaru, she has given birth to three children: Itachi, Sasuke, and Nanari. She is somehow assassinated by unknown individuals when Sasuke is about 7 or 8.
Fire Country manages not to fall to the initial wave of conquest, and forces Orochimaru to a temporary ceasefire. Sasuke and Nanari are sent to Konoha as "an implication of goodwill," and become friends with Namikaze Naruto, son of the Yondaime Hokage, Namikaze Minato. Talks and negotiations are held, but break down after a peace of 4 years -- it becomes obvious that Orochimaru plans to exploit Fire for "a resource of local abundance." The Hokage attempts to make a final stand against the Sound, but dies under mysterious circumstances. Subsequently, the nation collapses under the strain of Orochimaru's attacks. It is redesignated as "Area 11."
6 years later, Sasuke and Nanari live as civilians in the Concession of Toukyou, the administrative capital of Area 11. They are hosted by the Hokumon Group, originally a bloodline family of the Sound that fell out of favor with Orochimaru due to their alignment with Mikoto. The only daughter of the Hokumon family, Tayuya (voiced by Viletta's voice actress in Naruto anime, btw), has been raised as a civilian, and is student government president in the academy her family runs.
Sasuke was never formally trained as a ninja -- civilian practice of ninjutsu is outlawed, and all ninjas native to Fire Country who have not surrendered their nationality to become honorary citizens of Field are considered Missing Nin and by extension rebel terrorists. Said "terrorists" have formed an organization called the Fire Liberation Front, lead by Danzo. The strongest jounin-level team within the FLF is lead by Morino Ibiki.
During an incident caused by said terrorists near the Ghetto of Shinjuku, Sasuke comes across a seemingly immortal green-haired girl who claims the name "Madara." She forms a contract with him that grants him use of the Sharingan, but because he has no knowledge of chakra shaping, he only has access to a form of intuitive genjutsu that allows the planting of commands in another person's mind. Sasuke uses this ability to become the masked revolutionary leader known as "Rei" (Zero).
"Uzumaki" Naruto (he uses his mother's maiden name to prevent association with the late Hokage) has as of present become an honorary citizen of Fields and a genin of the Sound. He has grown up facing the hatred of his native people, and puts on an exterior persona not unlike how he is in canon. He seeks to someday become the Otokage so that he might change the Sound Empire for better. Shortly after encountering Sasuke again in the Ghetto of Shinjuku, he falls unconscious due to injury. Deep within the ruins of the Ghetto, his body comes into contact with an ancient tree that has been turned into a vessel for the Kyuubi using variant of the Shiki Fuujin. The creator of the seal was of the Namikaze bloodline, and keyed it to respond to his own family. Contact causes Naruto to become the new vessel.
Naruto is recovered by two medic nin of Sound -- Yakushi Kabuto and his assistant Karin. Kabuto takes an interest in Naruto's special condition and takes him on as a subordinate / experimental subject.
Misc:
The Nation of Wind (equivalent here to the Chinese Federation) is the second largest power on the continent.
Gaara's father remains Sunakage at present.
The Empress of Wind is Tenshi (unchanged from Code Geass).
Sakura's father betrayed Konoha and became an honorary citizen of Field and a Sound jounin.
Surface-Sakura is a civilian student at the Hokumon Academy.
Inner-Sakura is chuunin-ranked "missing nin" working with the Fire Liberation Front.
The leader of the cell she's a member of is Iruka.
Deidara is a civilian reporter of Field.
He becomes a fanboy of Rei and eventually joins up with Rei's group as an explosives specialist.
Madara claims the name "Tobi" when speaking with other individuals besides Sasuke, because there is a reputation associated with her original name. Nagato was a young boy Madara came across while travelling through the Country of Wind. She helped him master his bloodline limit, the Rinnegan.
Sasuke does not subsequently obtain increased functionality out of the Sharingan, though after repeated use, the control aspect does become permanently active. Itachi does not possess the Magenkyou, but is personality-wise identical to canon. He is considered to be next-in-line to the position of the Otokage. Following Mikoto's assassination, Orochimaru somehow gains the Sharingan. Nanari is, of course, blind.
Roro is a boy who was given a transplanted Sharingan at a young age by Orochimaru. Nominally, he is a genin, but his actual rank places him within the assassination unit of the Oto ANBU. He has intuitive access to a variant of the Tsukuyomi that pauses the subjective experience of time in a victim, but cannot use other aspects of the Sharingan's abilities.
The Hyuuga family was mostly destroyed during the war. A portion of the survivors surrendered and became honorary citizens of Field. Hinata is in the student government of the Hokumon Academy. As of present, she has a one-sided crush on Tayuya. She is secretly researching ninjutsu -- specifically, a highly advanced form of Kuchiyose that is thought to have been lost. Neji is probably a chuunin with the JLF
I'm missing an Orange and a Viletta (Anko?). Shirley = Tenten? Kiba = Rivalz?
Kaguya (unchanged from Code Geass) is a relative of the late Daimyo of Fire (who was killed in the war).
Kirihara Daizou might be the Sandaime under an assumed identity.
Euphemia and Cornelia have no equivalent either ...
I have no idea where Jiraiya and Tsunade are. Kakashi is missing too, but for obvious reasons, he doesn't have Sharingan.
There's a possibility that Jiraiya will end up guilding Naruto as in canon, and thus indirectly (possibly unintentionally) aid Orochimary's cause.