Well, to tell the truth, the second season of Code Geass takes place after 1 year of the first season. Because of that, I've been wondering about what happened in the end of season 1.
Here's an example I am curious: Kallen, now knows that Lelouch is Zero, still helps him in the second season. I have a theory about it that in the end of season 1, she has recovered from her shock and humiliation about Lelouch's secret. When he asks her why is she helping him after the revelation, Kallen replies that she may found out his secret, but doesn't care. Besides, Lelouch still leads the Black Knights. I guess this is how she is still supportive of him in the second season.
Well, think of something for the original plot of R2.