This is a good story, but I'd like to point out some flaws...
1.When Lelouch goes to talk to Milly, shouldn't she be more shocked and frightened? Because he was a tyrant and people were scared of him, so I would think that she would be more shell shocked.
2.Shouldn't you specify if Lelouch was brought back to life or if he was just "hiding in the shadows" for 18 years?
3.C.C doesn't show that much emotion, so I wouldn't of added the exclamation marks in her sentences because she acts like nothing can stun her.
4.Make some of Lelouch's sentences more sophisticated, because he didn't get shocked too easy, and had more of an, "answer a question with a question theme" so I wouldn't of made him sound so relaxed.
5.WTF????? Kallen and Lelouch? Come on!!!! (This is your story, but still, we know almost nothing that says that they really had feelings for one another.)
6. Could you explain more about some of the minor characters? I was confused a bit about who was who's child.
7. I can't remeber who Isaac is, (I do remember the name, but not the character,) so could you remind me, and tell me why he would be the antagonist?
8.Why would there be a guy named Zach in Japan? Not really Japanese...
9.How did Isaac take down Zero's guard so easily?
10.Why does Isaac want the World's Power to be restored to it's former self?
11.I think that Kallen would do a little more "puching and kicking and shoving Lelouch to the ground" when she first see's him again, and then starts to cry.
12.Mabye edit some of the words, to make it a little more Code Geass-E?
13.When did Lelouch have Sex with Kallen?
14.Maybe say a little more about the new type of Knightmares (since it's only been 18 years....)
15.I just don't see Kallen getting so emotional over Lelouch's comeback, plus, I really don't think that she would tell him that she loved him as soon as he came back. (That would be pretty awkward.)
I'm sorry to list so many things that I spotted, but I just would like to see this if they made this the R3, but this is your story, so don't change if it you don't want to. Beside all of this, it is a pretty good story, (the only weird thing that I'm not capable of coping with is that Kallen and Lelouch thing, it just seems so sudden, and I just don't see it happening, maybe more of a Lelouch and C.C thing? Still, great story.