There's actually two mangas. 'Lelouch of the Rebellion' and 'Suzaku of the Counterattack'.
The one I mainly follow is the 'Lelouch' one, which has changed some things from the anime version. For example Suzaku at the beginning is already attenting the same school as Lelouch, C.C was being transported on a plane/jet that crashed, the rebels try to vandalize the school one night which is when Lelouch realizes that Kallen is a rebel (and he ends up helping them escape). I like it but I find the art isn't as pretty as the anime (they look younger in the manga).
The 'Suzaku' one also slightly differs from the anime but has art closer art to it. It starts when Suzaku finds Lelouch in the crashed truck (in this version, like the anime C.C is on a truck). Lelouch doesn't have to escape like he does in the anime though and he takes C.C with him since he knows she's alive (at least I think he knows she's alive but I've only seen the raw of it). Zero appears a lot sooner in this version by attacking Clovis' limo and killing him.