Its probably going to be like this: Rollo is probably the partner of one of the undiscovered witches but got mindraped by the king and became his loyal servant. Later he figures Rollo will be a perfect substitute for Nunally and makes him think he really is Lelouch's brother. Then he mindrapes Millay, Rivalz, and Shirley, and the teachers and swaps out the entire school's population for other people and throws Viletta in as the watchdog because she can't be Geass'd. And I assume tablefap avoided being Geass'd and became their nuclear scientist. All as an elaborate scheme to get C.C. which fails miserably and leaves Lelouch with Rollo and the Black Knights again and the battle begins anew.
I do wonder what they are doing with Nunally though. She should be thoroughly useless since the emperor threw her away like trash years back. Unless she's just a hostage, but that's just anticlimactic and I doubt it's the case.
Anyway it will be fun if/when Lelouch finds a way to restore everybody's memories and he accidentally gives Shirley all of hers.