After watching the memory bit with Suzaku, I had assumed that Lelouch had already been shot in a non-vital area. He sounded tired and in pain. (As a lesser detail, if you look carefully, Suzaku's gun is pointed off-center, towards Lelouch's right shoulder, which is an ideal place to shoot Lelouch in order to keep him from using his gun.) If Suzaku ended up capturing Lelouch, a few details (IMHO) would fall into place.
As I've mentioned before in a previous thread, I got from someone on the AnimeSuki boards that Suzaku got his Knight of Seven position as a result of bringing Lelouch/Zero before the Emperor. Given that the Emperor has geass, it would make sense that he could do something WTF to Lelouch. And given that the Emperor knows who Zero is, he can marshal the powers of Britannia to use Lelouch to ensnare C.C. If he believes that an amnesic Lelouch is harmless, then he can still use him much like he did in this episode.
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As I've mentioned before in a previous thread, I got from someone on the AnimeSuki boards that Suzaku got his Knight of Seven position as a result of bringing Lelouch/Zero before the Emperor. Given that the Emperor has geass, it would make sense that he could do something WTF to Lelouch. And given that the Emperor knows who Zero is, he can marshal the powers of Britannia to use Lelouch to ensnare C.C. If he believes that an amnesic Lelouch is harmless, then he can still use him much like he did in this episode.