I think the implication is pretty clear: Lelouch was brainwashed into Julius Kingsley some time before episode 2 of Akito. After the end of episode 3, he would serve no further purpose to remain his Julius Kingsley persona, so he's brainwashed again back into a schoolboy. No further explanation necessary.
...Not to say that I wouldn't like to see more Lelouch. Or get some more explanations about the origins of Geass, like we were teased about in episode 3.