Kitted out in a serial-killerish rubber apron and gloves, holding an axe, Peter surveys the victims he's dragged indoors. He and Anne chop them up. Peter bellows a lot. As Peter showers off the gore, Anne decides it's a great time to join him and get some, because she's crazy and so is Peter.
Afterwards, Anne helps Peter dress. There's no going back now, he says. She points out that the world he came from never gave him anything, an assessment Self-Pity Petey is happy to hear. Anne keeps blabbering that Peter's "reborn; ascendant" and under his guidance they'll take back the abbey. Peter: "Why stop there?" The whole world "is soul-seeking" -- why not heal them, too? Uh, because you're … bonkers? Bonkers enough that he thinks breaking through the naval blockade is an option. If they are trapped on Killigan's Island with the CDC as Anne says, though, the plan is to steal the mycosis cure and then "eliminate them."
Alan injects Kyle with the antidote, then hands him a vial of it: Kyle needs it more than Alan, and so does the Coast Guard. Kyle is abashed: "I tried to kill you yesterday." Alan shrugs that off as the pathogen's fault. Kyle says regretfully that, after the dust settles, he still has to turn Alan in. Alan proposes turning himself in, if he can borrow Kyle's gun right now. Kyle needs to know what happened in Paris; Alan whispers that Box 274 at First Bank of Atlanta has all the proof Kyle needs.
Jules has run every possible test, but: Mother's dead. Sarah's preoccupied with the fluorocarbon solution she's injecting into the Immortaletus's jar. She'll have to do it every half hour forever to keep Immie alive, but she's okay with that. Alan comes in and stares at Immie, asking if that's "your … our child?" Jules is like, "Awk!" and splits.
Anne and Jules look at a painting of Mother as Anne relates the original tree's medicinal properties and how Michael spent decades studying it. Jules thinks the tree's location might yield seeds or something else helpful, but Anne doesn't know where it is; the painting is 300 years old, and "the tree is long gone." Jules can look at Michael's ledgers, though, if "Eli" gives his permission.
"Eli" is Peter's new cult-leader name, apparently, and he's staring self-importantly out the window of Michael's office. When he turns around, Jules, bless her, starts giggling: "You're kidding, right?" Peter is, unsurprisingly, not amused. "'Eli' means 'ascended,'" Anne croons. Jules: "I don't care what it means." Heh. Peter sniffs that he's found a higher calling and says Jules can look at the ledgers -- in exchange for protection from Ilaria for his followers, and a royalty on the sale of the infertility apple. "Looks like you're still Peter after all," Jules snorts, by way of agreeing, and leaves as Olivia comes in with the baby. When Jules is gone, Michael tells Anne to gather the followers and have them arm themselves: "It's time to take care of our CDC problem." Olivia looks schemey.
Then she runs into friends-again Kyle and Soren in a hallway and pulls Kyle aside: he and the other CDCers need to beat feet, pronto, because once Eli/Peter gets the cure, "you're gonna end up in a barrel." She gives him a bag of Coast Guard gear, including a radio. Why's she telling him this? He and Alan saved Soren. Her debt repaid, Olivia hurries away.
Alan wonders what kind of life Immie has to look forward to, but Sarah's determined to get off the island and to find a way for Immie to grow. Why doesn't Alan come with her and help her? He can't. Sarah has a fit and dares him to kill her, since he's so obsessed with murdering Immortals. He pulls Kyle's gun and says he has to finish what he started.
Jules cuts the Mother portrait out of the frame in one hallway while, in another, Olivia tells Soren she's trying to fix a big mistake and asks him to hide in his old hide-and-seek spot. He wants to help her and Kyle but she makes him promise.
Alan lurks up behind Jules in the botany library, claiming he's there to apologize for the day before. He offers his help, but is skeptical about the painting; they don't know if the scale is accurate, etc. Jules mentions that Michael was a painter, cartographer and astronomer, too: Could they use the stars in the painting to triangulate the tree's location? Alan grudgingly says it's "good work," and looks sad, possibly because he went up there to kill her and couldn't go through with it.
After a little "what the hell is that" comedy with Immie, Kyle breathlessly tells Sarah that Peter's lost it and they have to leave. She carefully starts packing Immie in a rolly case while Anne and the remaining Killigan's Islanders prepare for battle. Kyle blocks the door. Olivia looks nervous. The Islanders bust into the lab, but Kyle and Sarah have taken off …
… for the belfry. Sarah stops halfway up; Immie's jar has sprung a crack. Kyle patches the jar with gum and keeps heading upwards, but Sarah cry-voices that she has to get Immie another jar in 30 minutes or he'll die. Anne knows where there are more jars. Kyle gives in, saying they'll split up to find Anne.
Alan and Jules snipe at each other about who's more destructive to nature: humanity or Ilaria Corp. Jules sighs that there's no defeating Ilaria: they're everywhere. Alan wonders if maybe Ilaria's alleged omnipresence and omnipotence is just that -- propaganda. He killed all those Immortals for her, and would have killed ten thousand more. She basically says she couldn't love Alan back fully because she didn't know her effed-up family history while they were married, or something.
Peter's putting the baby down when Anne fearfully reports that the CDCers "have fled" and taken the cure with them. They figure out that Olivia warned the CDCers. Anne is to keep looking for them; Peter will handle "everything else." "Show no mercy," they repeat to each other before kissing. Weirdos!
Alan and Jules figure out that the tree's there at the abbey while Kyle almost gets caught by Peter. Soren yanks him into a closet at the last second. Right outside, Peter makes nice at first as he confronts Olivia about betraying him, but when she tries to run, he breaks her neck. Kyle clamps a hand over Soren's mouth and tries not to hurl. Soren is devastated, of course, and Kyle tries to get him moving and comfort him: it's not his fault, and Kyle's "his family now," if he wants.
After a cursory sweep of a dorm room, Anne gets mugged by Sarah and ordered to tell her where the rest of the baby jars are. Jules, meanwhile, is with Alan in the caf, asking what Michael was like. She deduces based on Alan's description of Michael as a narcissist that he built the abbey on top of the original tree. Pulling up the floorboards reveals a huge stump. Alan knows the tunnels underground; that's probably where Michael accessed the root system.
Sarah snarks that it's no wonder Amy turned out how she did. Anne snarks back that Immie isn't a real child and Sarah isn't a real parent ... and calls Sarah's bluff on using the machete, so Sarah buries it in Anne's foot.
Cut to Anne shuffling into the Organic Baby Farm Basement, what she calls Michael's "highest achievement"; Sarah is revolted, especially when a toothless "vessel" snarls at her. Sarah finds the life-support jars, then orders Anne to release the vessels.
Peter tells the baby a whiny story about wishing he were a changeling as a kid. "Blood is meaningless," he announces to no one, and says the baby is his son, his family. Poor kid.
Jules and Alan climb into the root system. Jules still isn't finding any signs of life; Alan duhs that it's a stump, not a tree, and probably died generations ago. One of the vessels looms up on them, then dashes off …
… as Kyle sends a distress call. Sarah reappears, and Kyle asks about the bloody machete. "I'll tell you after about five years of therapy," she pants. One of Kyle's hails gets an answer; he's ordered off the military channel he's using. He says he has a cure and is put on hold for the captain.
Anne drags the bloody remains of her foot into Michael's office and tattles on Sarah as Peter fashions a crude tourniquet. Sarah made her go to the Baby Farm Basement and release the vessels; now she and Kyle are trying to escape. Peter asks where they are now, but trails off when he hears choppers.
As helicopters approach the abbey, Jules spills test enzymes onto the ground. They glow, which means "Mother is everywhere." We don't really know what she's on about, but we guess it's a good thing. Also good, at first, is the fact that a chopper is lowering a basket towards the belfry to let Sarah, Soren and Kyle escape … until stupid Peter starts shooting at the chopper and it flies away.
Jules explains that she doesn't need the roots, only the soil with the enzymes in it (just go with it) and raves about the infertility potential of the discovery. Alan furrows his brow, pulls Kyle's gun, and says he's sorry. Jules asks what he's doing. "Stopping Ilaria," he says. She argues that she's doing that too, which he doesn't buy, and she keeps stalling while pulling her own gun from her bag.
We go to black, and then hear a shot fired. DUN!