Amy is performing certain ministrations on Brother Landry with her hand; in exchange, he's giving her a gasping report on the CDC doctors (worried), Isaac and Soren (they've "completed their paths" -- i.e., died), and Anne (thinks she's losing control of the situation). As Landry gets closer to, uh, completing a path of his own, Amy talks about her mother Anne's control issues, and says it would be a real shame if something unexpected were to befall the CDC team, by which she means the opposite. It's time for them to take matters into their own hands, she says. Ha ha. Also, gross.
At a cabin in the woods, someone is splitting wood. Aerov (!) strolls up to the porch, singing, and says something's got the local deer spooked. Jules's mother, Jaye, comes out and teases Aerov about his terrible singing. Aerov freezes: "Father, someone's coming." The wood-splitter turns around -- slowly, thanks to the seventeen pounds of hair extensions he's sporting -- and we see it's Hatake (!!). He orders them both inside, but when the camera wheels around, there's nobody there.
Michael removes a root structure from a box in a wall safe. He's apparently using it to repair a gash on his finger, but he and Anne are interrupted by Peter demanding to know where Soren is. Anne disingenuouses that Soren was under Peter's care, and when Peter impatiently asks for the manpower to do a coordinated search, he gets a long speech from Michael about grafting instead. Peter openly rolls his eyes and snaps that he'd better not find out they caused Soren's disappearance.
Peter stomps off, and Michael asks Anne if they did cause it. Anne denies it and reassures Michael that all she cares about is protecting their way of life. Michael pretends to nuzzle her but puts his hands around her neck in a sinister manner and talking pointedly about having a difference of opinion.
Sarah has morning sickness and stares at her black-veiny belly, then heads to the lab to keep testing for the pathogen. She and Kyle bicker about his calling her "Hot Zone" and she complains that it could take weeks to isolate the germ with this equipment. Blah blah science blah, Kyle suggests matching Soren's samples to those of the ship victims. Sarah admits that could work…but now Kyle can't find the ship samples in his bag, theorizing that they fell out at the shack. Sarah flips out: "Those samples were everything." She's happy to tattle to Peter about it, too. Kyle's set to head to the shack and retrieve them, but Peter needs Kyle there, using his rapport with Amy (is that what the scientists are calling it these days?) to get more information on Soren's symptoms. Before they head out, Kyle hands Sarah his gun.
Meanwhile, in the future, Jules pauses for a sip of water and soon finds Hatake's axe at her throat. He knew they'd send someone; he didn't think it would be her. Jules convinces him that Ilaria's "gone," and she was wrong to trust them, but she and "Father" are on the same side now. She's trying to save the few Immortals remaining from the TXM7 pandemic. Why should Hatake believe her? She's unarmed, she says. Hatake looks unconvinced, but drops the axe.
Alan is raking and staring at wine barrels getting rolled into a delivery bay. He's told by the Brother in charge that no alcohol is allowed on the island, and it's better not to ask what's really in the barrels.
Kyle's apologizing for hurting Amy's feelings; Amy's lecturing him smugly on the cult's commitment to free exploration of ideas or whatever. Kyle gets right in her face about how he usually gets the answers he's looking for, "one way or another." Cut to Kyle taking blood samples and questioning a girl named Lizzie about Soren. Lizzie is apprehensive about talking with Amy lurking nearby, but reveals that the day he got sick, Soren said he was scared. He broke a rule; he didn't want to go in "the pit." Kyle asks what rule, what pit, but Amy looms over them and Lizzie clams up.
Sarah and Peter hike to the shack. Sarah thinks they should bring Alan into their investigation. Peter thinks Alan is manipulating Sarah, adding that Alan's obsession with Jules led him to kill innocent people "Immortals. Just like you."
Landry looks on as Amy, masked and gowned, harvests a berry of seraphim's breath (used in human sacrifice, it drove its victims to bloody suicide), and blah-blahs free will. She grinds the berry and puts the contents in a pot. Landry asks if Michael and Anne know "about this" (they don't), then what he's supposed to do with the pot.
Cut to Landry asking the kids to gather round to play a game, "Time Machine." Lizzie "gets to" go first, and Landry takes out the pot, attached to a mask, and tells Lizzie to breathe. Her eyes flutter. Landry smiles creepily.
At the shack, Sarah and Peter discover Leila's body has been removed. She's gathering the samples and talking about Kyle's "inspired" testing idea when something attacks the shack from outside. They brace the door and escape out a back window -- almost. Peter is tackled not far from the shack by a pathogen carrier, and the guy's about to eat Peter's face when Sarah shoots him.
Back in the future, Hatake makes tea in a World's Greatest Dad mug, smirking. Aerov tells him that Julia "can't be trusted," though Hatake assures Aerov he's got it in hand. On the porch, Jules eyeballs the two mugs, then takes Hatake's, presumably to make sure he's not going to drug her -- which he could still do by predicting she'd take his mug and dosing "his." They chat about Hatake's having found peace, and the mixed blessing of being immortal. Then, sure enough, Jules abruptly collapses, protesting, "You drugged me!" before passing out. Hatake, still smirking, sips his tea.
In the present, Kyle is wondering aloud why Soren's blood sugar was so high when Lizzie lures him out to the woods, claiming that "the children are sick." The Brady Bunch's "Sunshine Day" comes up on the soundtrack as Kyle is surrounded by the tripping brats of the abbey and stoned, Old Testament-stylee.
While Alan tries and fails to snoop around the delivery bay, Peter is ripping Michael a new one for not telling them "there are people in the woods" -- people suffering from what looks like ergot poisoning, Sarah adds. Michael BSes them about the people who "choose to leave" the abbey. Peter and Sarah are disgusted that they're left to fend for themselves out there. Sarah theorizes as they're stomping back to their lab that the pathogen started inside the abbey.
But right now, they have a bigger problem: the bloody heap of Kyle in the lab. "'Sunshine Day,'" Kyle pants, struggling to sit up as Peter and Sarah tend to his wounds. He describes the kids and their blank darting eyes. Peter wants to see them for himself.
In the future, Jules wakes up in a wheelchair as Hatake is brushing her hair and filling her with sodium pentothal so she'll say why she's really there. He doesn't buy that she's looking for a cure for the Immortal-killing disease, until he sees the rash on her breastbone. Jules is passing out again when he asks who she works for. "Ilaria," she slurs.
The CDCers come to the kids' bunk. "Sunshine Day" is playing, but the children seem fine. Lizzie runs up to Kyle, hugs him, and asks what happened to his head. Kyle pulls a baffled face. At the lab, the docs spitball what might have caused the attack; Kyle rightly concludes that someone wants them off the island. Sarah spots something under the scope: a fungus, one they don't recognize. She renews her plea to bring Alan on board. Kyle, loading his gun, is surprised to learn Alan's on the island (and not psyched nobody told him); Peter gives in, but wants to talk to Alan alone first.
Alan himself is stealing a guard's keys so he can find out what's going on with those wine barrels while, at Hatake's Interrocabin, Hatake and Aerov argue some more about Jules. Jules eavesdrops blearily as Jaye says a lot of mysterious things about "making her understand" and how Jules "doesn't belong here." Aerov glares and storms out.
In the dark of night, Alan lets himself into the delivery bay and finds the rows and rows of bottles we saw during the dental extraction in Episode 1. He pries open the casks, and they're empty, but he does find a molar stuck to the inside of one of them. He's peering at it in confusion when Peter whangs him in the head with his own crowbar. Oops.
The Jackson 5 accompanies Jules coming to again. Hatake's dressed her in a red frock, and he wheels her up to the table for "family dinner." "Say hello to your mother and brother," Hatake says. He's seated a horribly burnt Jaye and the grisly remains of headless Aerov at the table as well. A revolted Jules screams us into the end credits.