So, the emporer brainwashes Lelouch and puts him back into a school where he knows most of the people and some even know he's Zero, with undercover agents assigned to watch him for signs of C.C. contacting him.
But of course, the Emporer doesn't go and wipe the rest of their minds about who Nunnaly is or plant false memories of Rolo.
It was just magic, makes perfect sense.
Seriously, you were one of those people who needed to play FSN visual novels to figure out Archer was Shirou right? jesus christ.