A New York state police officer picks up a kid wandering down a backwoods road by Edina. Seems like the kid, Teddy, is running away, but he stays mostly silent. The trooper is driving him home when suddenly the kid is no longer the cherubic youngster, but a deformed creature in his back seat. So it's off to the station they go, with the other officers talking about how this kid must be one of them. But before they can do a whole lot with the knowledge, a couple of adult freaks burst in with shotguns and kill all three officers, and take the kid away.

So the Fringe team swings in to action, even though Walter's still freaked out from previous events -- no, not seeing Charlie alive and well just a little while ago, but watching chunks of his brain die. Turns out there have been rumours of deformed people in the area going back 30 years. There's a military base nearby and a strange low humming in Edina, but those are just turbines, right? Nothing to do with anything, right? Meanwhile, Teddy's back with his parents, and he looks normal again, but the Fringe team doesn't know that yet.

So the Fringe crew gets run off the road and Peter's the only one conscious enough to return fire at the freak with the shotgun. Peter manages to wing the guy, and when reinforcements arrive and the area is searched, they find Teddy's dad, dead of a gunshot wound. Walter, however, is more interested in a pretty butterfly that he wants to bring back for Astrid, who is all of a sudden really interested in butterflies. So when Walter gives it to her and it's just an ugly moth, Walter starts recalling details about military testing (that he turns out to have been involved in, naturally) in the late '70s, a human camouflage-type project that instead just disfigured everybody. Sick with guilt, the lead researcher was able to use an electromagnetic pulse to scramble people's optic nerves slightly so that the freaks seem normal. That's what the humming is. No, it really doesn't make any kind of sense.

While Walter and Astrid find and shut down the pulse generator, Olivia and Peter get in a shootout with the previously helpful sheriff who, to the surprise of no one, is involved, but he's killed by Teddy's mom (the daughter of the scientist, whose experiment was expanded by the military without his knowledge), who's sick with guilt over the deaths of innocent people to keep the town's secret.

Walter gets his groove back by the end of the episode and pleads with Broyles to keep the investigation quiet, since the people involved with the killing of the police officers are dead now. Broyles tries to be cool about it, but since he always seems kind of pissed, Walter needs Broyles to pretty much spell it out for him that if Walter never found the generator, then there's nothing to report, is there?