After four episodes sans Peter, “Novation” is a pretty low-key episode considering the circumstances. Peter is off to the side for majority of the episode, interrogated a couple times but in his cell the entire time. The characters’ response to him is actually realistic; they have no clue who he is, but he’s not an imminent threat, so they don’t make a big deal out of him. It’s also good that Peter is a smart guy and figures the situation out almost instantly, and does cause a big raucous trying to convince everyone they know him.
The problem with the episode, though, is that the new shape-shifters don’t really make good enemies. I like that Peter helped on the case, but the conclusion of the episode is rather tepid: now they can’t know who’s a shape-shifter unless they perform surgery on them. I’m sure they’ll come up with a solution sooner or later. The larger problem is that they’re part of the larger mythology of the show–something that’s always been nebulous at best, changing at the writers’ whims. It’s pretty obvious the writers make stuff up as they go–evidenced by the random forays into the pattern, the Bible, etc–so it’s hard to gauge anything about the plot.