The episode starts off with Joshua finding his way to Max with his canine sense of smell. Asha Barlow says a couple of derogatory things about Max and the other transgenics. A mutant with a mutilated face and bleeding skin goes around in China Town, believed to be infecting people. He gets shot while saving a boy at a motel and, during an autopsy, is believed to be clean of any infecting agents. Asha gets caught while trying to illegally get through a sector checkpoint and is rescued by Max. Joshua stays at the Sandman's house to avoid getting seen in public. The infection is later determined to be an infection agent deployed through a hand-held fireworks launcher targeted at specific gene patterns. The plan to deploy an infection agent targeted at transgenics is foiled by Max and Logan.
A night of Halloween trick-or-treating is the perfect cover-up for Joshua, who is delighted at the opportunity to get out of the house without attracting attention. Rafer and Max grow closer while encountering transgentic Manticore creations.
Max and Logan finally trace Ames White's son to Brookridge Academy only to find him involved in a mysterious cult ceremony taking place in a temple on school grounds. At the same time Sketchy gets a job for the mutants magazine and is on the look out for mutants from Manticore, and Max and Alec are getting worried.
While Joshua befriends a blind girl named Annie, Max struggles to deal with her overwhelming guilt when Logan nearly dies after unintentionally touching her. Meanwhile, Alec is arrested for a murder committed by his twin Ben.
White uses Max's clone to track her down as increased tensions force Logan to flee from his apartment forever, Max to leave Seattle and Joshua to make his way to a place where transgenics don't have to hide - Terminal City.
The gang at Jam Pony find out Max and Alec are transgenics after a young X6 and a pregnant X5 take cover inside the building and an angry mob and police gather outside. This is the series finale, as the show was cancelled afterwards by FOX and not renewed for a third season.