Actually,they're four acording to Wikipedia.
Manga
Kadokawa Shoten has published four separate manga adaptations, each containing an alternate storyline.[26]
The first, Code Geass: Lelouch of the Rebellion, by Majiko~! and originally serialized Monthly Asuka, focused on the protagonist of the series, Lelouch Lamperouge, with few differences from the anime storyline with the exception of the Knightmare Frames not existing. The manga does not share the same staff or creators as the anime and is often considered a different reality from the anime because of the many significant differences.
The second, Code Geass: Suzaku of the Counterattack (コードギアス 反攻のスザク Kōdo Giasu: Hankō no Suzaku?), written by Atsuro Yomino and serialized in Beans A magazine, focused on Suzaku Kururugi in an alternate reality, where he wears a human-sized enhancement suit provided by Lloyd as Lancelot, a masked government-sponsored superhero, who fights against the criminal organization known as the Black Knights.
Code Geass: Nightmare of Nunnally (コードギアス ナイトメア・オブ・ナナリー Kōdo Giasu Naitomea Obu Nanarī?), serialized in Comp Ace and written by Tomomasa Takuma, focuses on Lelouch's sister, Nunnally.[26] When Lelouch goes missing in the incident at Shinjuku Ghetto, Nunnally encounters an entity called Nemo, which restores her health and grants her the ability to summon the Knightmare Frame Mark Nemo. Using these, Nunnally attempts to seek out the whereabouts of her brother, but arouses the interest of the elite covert-ops Britannian Special Foreign Legion "Irregulars," which seeks to capture or kill her.
The most recent manga adaptation, Code Geass: Tales of an Alternate Shogunate (幕末異聞録 コードギアス 反逆のルルーシュ Bakumatsu Ibun Roku Kōdo Giasu Hangyaku no Rurūshu?), was serialized in Kerokero Ace. Set in an alternate 1853, with arrival of Britannia's Black Ships appear in the harbor of Uraga and Lelouch Lamperouge (琉々朱・爛縁侍 Rurushu Ranperuuji?) as the commander of the Shogunate's military counterinsurgence brigade known as the Shinsengumi, which fights the Black Revolutionaries (黒の騎士団 Kuro no Kishidan?), a rebel group led by a mysterious masked individual known as Rei (零 lit. Zero?) (these two organizations turn out to be one and the same, seeking to combat influences of Britannia). Geass is the ability to call upon and summon the armored entities referred to as Knightmares (ナイトメア?), of which Lancelot (ランスロット?) is one.
Three of these manga series have been licensed for an English language release in North America by Bandai Entertainment.[27]