At a local church, an altar boy, Gary, stabs a priest, Father Downey, with a boxcutter. Gary goes to a park and washes the blood off his hands in a fountain and throws his jacket and tie in the dustbin.
The squad quickly hears of the incident and after seeing the body at the mortuary, head for the school. Gary is 12 years old and up until 6 weeks ago, he was talking about the priesthood. Michael talked to Gary's classmates, encouraging them to speak up if they know where he is. Rice opens the window's blinds and he and Michael note the class' subtle reaction to the sunlight. Michael dismisses the attack, as a cop he saw kids do terrible things, it doesn't make it a Code V case. Or it could be meningitis, they'd find bright light painful, causes mood swings. Angie arrives to test the children. She counters Michael's theory – meningitis presents over days, not weeks and has a reaction to all light, not just sunlight. She assures Michael they're not jumping to conclusions.
Jacob reports to Kirsty that Michael has completely disappeared, as if he'd entered witness protection. Shutting out Kirsty was just the beginning and Michael's family's not talking. This is good news – this is confirmation, they're not paranoid. This squad's got a lot of clout and probably has government backing. What they need is luck, someone from Michael's life before who'll talk – old friends, contacts, old flames? Kirsty thinks of Frances.
A paedophile, Colin, finds Gary crying in a public bathroom and takes him home with him. Colin's dog Maxy has a strange reaction to Gary, attacking and biting him. Panicked, Colin takes Gary to a hospital and leaves him there. Colin returns home and puts all of his video tapes and magazines into black rubbish bags and has a bonfire outside, burning it all.
Michael and Rice talk to Gary's mother. He's been acting strangely the last few weeks, suddenly stopped being an altar boy, avoiding Father Downey's calls, and gets angry in the morning when his mother opens the curtains. At the school, Angie takes samples from the boys and notes the boy has no reaction to a mini flashlight in his eyes. She picks up a Bible and she asks him to open it. The boy is clearly terrified and starts to hyperventilate. Michael and Rice return to the school to find that Angie's quarantined all the boys. Michael angrily challenges her but she says they have to be sure. Rice gets a phone call that Gary's turned up at the hospital, bitten but not how they would think. Michael interviews the soccer coach who defends Downey, saying he never say Downey do anything wrong with the boys.
Michael searches Downey's house and finds a disk which pictures of boys on it and then pictures of Gary sitting on a bed somewhere. He shows the photos to Rice, Angie and Harman. Michael confirms the bedroom in the photos isn't at Downey's. Harman suggests that the disk could have been planted. Michael angrily points out that Code Vs don't like churches but Harman counters by reminding Michael that not everyone who works for them is a Code V. Michael says there are two ways to look at this: 1 – Gary was abused by Father Downey, the other boys heard about it and they're showing stress. 2) Nothing – Angie found no marks on the boys. She insists they're infected, but she's not sure how. Angie recommends releasing all the boys except Gary, he's the worst infected. That way they can stick to the meningitis story. Harman accuses Michael of making lazy assumptions – find out where the photos came from.
Michael and Rice go to the park. This is where Gary's blood-stained shirt and tie were found. No witnesses of a dog attack or signs of blood so Gary probably wasn't attacked here. They notice the public bathroom and a sleazy looking guy come out. Could Gary have left with someone? They decide to check for local paedophiles who own dogs. Angie interviews Gary who will only say that Downey made him sick. When Harman comes in, Gary reacts badly, instantly knowing he's a priest. Harman deliberately provokes Gary and Angie asks him to leave. She later joins him in his office. Harman points out that the Code Vs couldn't cause mass infection the traditional way, maybe they've found another way, biological warfare?
Kirsty meets Frances for a drink. Kirsty knows Frances has been in contact with Michael. Frances talks about how Michael thought there was something going on with Jack's disappearance but he got that out of his system, that kind of thing can get obsessive – she looks pointedly at Kirsty. Kirsty realizes that Frances knows what's going on and asks that she be straight with her. Frances does – leave Michael alone, he's made his choice, and refuses to pass on a message. Kirsty tells her that she's not on her own anymore, that she doesn't need Michael's help and storms out of the pub.
Jacob, doing research in his paper's archives, is looking up articles about Angie and her husband Robert's death. He realizes he's not alone, seeing someone inside with him. He leaves, sure he's being followed. Kirsty calls him to say Frances wouldn't help and he says she shouldn't call him from her house phone, he hangs up. Scared, Jacob turns around and calls out to the dark and a man steps out of the shadows. Kirsty calls again from a payphone but there is no answer, Jacob's cellphone is in a dustbin.
Angie invites Harman over to her house to tell him about his test results – Non-Hodgkins Lymphoma. It's slow growing but incurable, but it's possible it could go into remission. He asks for specifics, how long does he have? But she evades, saying this is just the beginning of diagnosis, not the end. Harman notices Angie's daughter throwing a basketball into a hoop, on the balcony. Angie wouldn't let her practice at the leisure center at night so she lost her place on the basketball team. Angie has been accused of being an anti-social mother.
Rice and Michael are going door to door, checking out the list of local paedophiles with dogs. They find Colin who accidentally incriminates himself to Michael. Colin invites them to search his flat but Michael says why bother, he's had all afternoon to destroy evidence. Rice gets aggressive, slamming Colin into a wall – they're not cops, they can do what they want. Rice starts hitting him and Michael looks away. Finally Colin says he didn't touch Gary. Michael shows him the photo of the bedroom and Downey. He recognizes Downey who helped with the soccer team when Colin used to watch the boys play. Maxy had never attacked anyone before but Colin had seen him act strangely once before. He gives them a name and address, Oliver, who has a skin allergy and doesn't go out during the day.
Michael and Rice go to the address, getting the keys from the manager. They let themselves in and look around. They find the same bedroom from the photos. They note the boarded up windows and Michael finds the hidden camera. Rice finds a tv with video tapes and puts one in. Michael hears Oliver come in with a boy and looking at the tv Rice is watching, sees no-one in the room so goes in firing. He shoots Oliver twice and sees with horror that Oliver shows up on his gun's monitor but the boy doesn't. Rice comes running but Michael is in shock and the boy vampire runs out. Michael rushes to Oliver's side and tries to calm him. Taking him to the hospital, Angie says Oliver genuinely has a skin condition, he gets cancer from sun exposure. This is actually the closest version we have to what Code Vs have. Angie gently tells Michael to go home and he assumes he's suspended, but she says no, just go home.
Now that Oliver is stabilized, Angie runs tests and discovers that Oliver has a new strain of meningitis, which has been altered to carry Code V. Infection only requires close contact. The Code Vs can create an epidemic by making us the carriers. Oliver is patient zero, Gary contracted it from him. Oliver was the perfect guinea pig, our closest relative to Genus Code V. Oliver couldn't control himself and broke quarantine. As for Gary, a laser only works on a wound but Angie thinks she can make an anti-serum from Oliver's spinal fluid, Gary should be fine. Rice points out that Gary will be facing murder charges. Harman says that since the Code Vs framed Downey for being a paedophile to throw them off, they should use that to save Gary, framing Downey. Downey's dead and Gary has his whole life ahead of him.
Angie and Harman visit Oliver. In exchange for being their guinea pig, they gave him a boy who would never grow up, never tell his parents but it didn't work – he's not a real boy. Despite the fact Oliver was contagious, he went back to real boys, including Gary.
Michael goes home and sits brooding in his apartment. Frances arrives and tells him of her meeting with Kirsty. She researched Kirsty's new friend, Jacob, who wrote a book on missing persons. He's good and Frances got the impression that Kirsty's gotten close to Jacob. Michael says it won't matter soon, he's on his way out, thinking about the shooting. Later, Michael visits Harman and is stunned when Harman clears him of the shooting. In the hallway, Michael asks Rice how he goes about getting fired and Rice says it's not the fact that the paedophile was human that's scary, it's the fact that Michael fired two shots and still missed Oliver's heart. If Oliver had been a 'leech', Michael would be dead. Rice thinks that Michael has a lot of potential… if he keeps alive that long.
Michael goes to Kirsty's and sees her hugging Jacob. Inside, Kirsty makes Jacob dinner. He says her phone is probably tapped and that Jack got into trouble because he found out about a death squad. Kirsty is shocked at the thought Michael could be involved. Jacob just says that Michael's in up to his neck. Before he leaves, he goes into the bathroom and throws up the food he just ate. He meets her downstairs and kisses her. She protests it's too soon but then starts kissing him, then he starts kissing her neck…