It does make me wonder, yet again, what Scorpius's motivation is. He hasn't been given any real reason why he's doing all these weird things to John, why he's taking so much time and using so many resources to capture him. Why would he put a chip in John's head? Is this all because John resisted his stupid chair the first time he was captured? His actions just make no sense at all, atleast Crais had a reason to hunt John, even if it was kind of stupid. Scorpius just seems to have nothing better to do than to chase John. Besides that, this was a solid episode, and I think this will be a good group of episodes.
You would know the answers to those questions, at least to a degree, if you hadn't chosen to skip key episodes.