Flashback to three months prior. In a car at night, a woman hands Kyle a file on Alan and explains that Alan's "our responsibility" after the Waterloo in the Arctic and the bombing of Ilaria. Does "our" mean "the United States's"? "Ilaria's"? "We need your help to bring him in," the official tells Kyle.
Back in the present, Kyle rushes down a tunnel, a bleeding Sarah in his arms. He emerges into an abbey courtyard and tells Peter he found Sarah on the cannery floor. Killigan's Islanders stream out to gawk, but do nothing to help. Jerks.
At the infirmary, Grumpy Grandma Agnes takes over. Kyle doesn't care for the idea, but Agnes sniffs that he and Peter are "research doctors," and she's treated every wound on Killigan's Isle for 50 years, so unless they're thoracic surgeons, they'll "just be in my way." Burn. Peter and Kyle exchange significant looks for about two weeks.
After the credits, they stop staring and start arguing. Kyle wants them to leave the island pronto, warning the Killigan's Islanders about the infected honey on their way out; Peter's against, because Sarah can't be moved, and tipping the Islanders about the honey would create a panic. Not to mention the shroomosis virus or whatever it is isn't contained. Kyle's like, I got stoned by a bunch of rugrats, someone stabbed Sarah, and this is your concern? Peter mollifies him: he'll talk to Michael about the honey; Kyle can go seal off the hive. Yeah: splitting up under these circumstances is a top-notch idea, Peter.
30 years in the future, Jules comes to, gasping, and is scrabbling for the sword when Caleb appears to help her away while, in the present day, Michael reacts to the killer-honey revelation with skepticism. Not that it exists, but that anyone would disobey him by eating food from outside the abbey walls. Peter thinks now's a great time to 1) blow Alan's cover and 2) blame everything that's gone wrong on him, and when Michael refuses to pass judgment on "Brother Jerome," Peter snaps that Alan's a terrorist. Michael replies that the problems actually started when Peter arrived; doesn't make him a terrorist, "does it?" Well, that doesn't, but anyway, Peter admits that Alan's his brother, and suggests quarantining him. Michael says creepily that now he owes Peter.
Alan is awakened by the door to his room swinging open on its own. Having apparently never seen a horror movie, he goes into the hallway to look around, then back into his room, only to get jumped by Brother Landry and wrestled into a dungeon hole called an oubliette (drink!). Michael appears at the top grate to prattle about Alan confronting his past. Alan is confused and also worried that Michael's onto him; he offers that Michael said to leave his past "at the gate." Don't tell me, Michael says, crooking a finger: "Tell it to him." Alan sees a hooded figure sharing the cell with him; it's Peter, mentally adding another seventeen entries to his I Hate Alan slambook even though, yet again, this is his own fault. Michael says they obviously have a lot to work out, which they might do … or they might kill each other.
Michael leaves. Peter asks Alan to untie him. Alan's like, no thanks, traitor. Peter claims Alan was "the last chip" he had to play to get Michael to work with the CDCers. "Right," Alan snarks, before correcting Peter that it's his team Michael's stymieing, not Peter's -- and is it him, or does trouble follow Peter around? His buttons successfully mashed, Peter's all, but you blew up a building, and goes on a self-pitying "I went to the North Pole to get away from Jules and all I got was this lousy case of Narvik" rant. Alan does untie him, and after a few rounds of "it's not my fault I'm better at everything"/"that's not what your wife said," they start swinging.
Michael's demanding an explanation about the bees from Amy and Anne. When Anne, who has no idea how the bees might have picked up a virus or moved their hive, falters that sometimes Nature finds a way, Michael gives a speech about a plant called the suicide tree -- and starts to jam a blossom down Anne's throat. It's a harmless re-graft from Michael's lab, it turns out, but the point is, "on this island, Nature does" as Michael says -- and so do they.
In a cave thirty years in the future, Caleb sews Jules up as she explains that, while she's an Immortal, she's "not indestructible"; she can't grow parts back. She also tells him Hatake, whom Caleb knows as "the man who talks to ghosts," is her father. "You killed your father?" "We had issues." It's only February, but we may have our Understatement of the Year already!
In 2015, Sarah wakes up, asking for Kyle. Agnes checks on her, and wonders aloud at how quickly Sarah recovered after losing so much blood. Sarah tries to sit up, but can't: she's got various perforated organs. She runs her hand over her womb and asks about "permanent damage." Agnes doesn't exactly answer.
Amy chews Landry out for not telling her about the honey sooner as Kyle and his hazmat suit head to the orchard. He finds an young woman's body, or so he thinks, face-down in the grass -- but she's just bait. Kyle's set upon by her and several other abbeyites, and he manages to flee, but one last abbeyite rushes him right near the infected honey. He's throttling Kyle when a bee swarm neutralizes him.
As Michael admires a ladybug on his knuckle, Anne comes to apologize for biffing the honey/bee situation. Michael grandly forgives her, kisses her hand, and showers her with compliments while backhandedly noting "what the years have done to" her. Anne looks hurt.
The Fightin' Farraguts rest up after their brawl. Alan wonders what happened to them; they used to be a team, "against the old man." "We grew up," Peter grunts. Peter theorizes that Michael put them down there to beat each other senseless, but Alan thinks he did it to see if they'd find a way out -- the same unnatural-selection way he manipulates plants. If Peter stands on Alan's shoulders, and the grate isn't locked, Peter can pull Alan up after him … or the other way around, since Alan doesn't trust Peter "after all we've been through lately." Sucker Peter agrees to boost Alan instead.
Sarah's finding out from Agnes that she's (still) pregnant, and correcting her that the father isn't Kyle. Agnes makes various pronouncements about children and legacies.
Landry's smoking the bees to sleep as Amy dresses Kyle's bruises, then tries to fondle him again -- in vain, again. Landry glares at them as Kyle shoves Amy away; Amy snots, "I can play rough too." Landry sledgehammers the wall and starts pulling out the hive.
Caleb cooks campfire supper and backstories that his mother brought him to Killigan's Island after his father died in "the food riots." The outside world's only gone downhill in the interim, but Jules maintains it's not hopeless; she's trying to save everyone, mortal and Immortal. Caleb's like, sure, get a conscience now that you're dying.
Agnes harvests pollen in the botany lab and, when Sarah is insisting on going to check on her team, knocks Sarah out with it. She opens Sarah's eye to check her pupil, and finds the contact she wears to cover the silver eye. "It can't be," Agnes breathes.
Kyle, who hasn't gone looking for Peter or checked in on Sarah by the way, is testing honey when Landry comes in with a sample Amy wanted him to have. Kyle starts to bitch about Amy checking up on him, but changes his tune when Landry is a lovestruck weirdo about her. Kyle returns to his scope; Landry stares unsettlingly at him for about a month.
Amy chases down Agnes to whine about the bees; they need Agnes's help. "Find Anne. Deal with it," Agnes grunts; they have bigger problems. "The CDC doctor … is a silver-eye." That's impossible, Amy says. You're right, Agnes says. Amy looks afraid, or maybe she's just pouting again.
Alan balances on Peter's shoulders and scrabbling for the lock mechanism. He gets out, and stands for a very long moment, looking back down into the oubliette. It begins to dawn on Peter that he's the one who should have had trust issues, as Alan says he's only there because he had to save Peter in the Arctic; he's spent most of his life bailing Peter out. Peter babbles that he and Alan had a deal. Alan snorts that Peter would never have come back for him, so he's not letting Peter out until he tells the truth -- about Narvik in Puerto Rico, about Paris, about the Scythe. He's working for Ilaria, isn't he? Peter looks like he might vomit as Alan sneers that Peter sold his soul, and probably not for much, either. He slams the bars closed as Peter bellows.
In the future, Caleb checks Jules's temperature. They talk about forgiving her father, and Caleb perks up when she says Hatake called the sword his "legacy." He examines it, and though Jules claims she doesn't know what it says, it's unclear if that's the truth (or if Caleb can't read the symbols himself). She sleeps by the fire as, back in the present, Amy rewards Landry for getting her a jar of poisoned honey that will get her off Killigan's Island with, uh, some poisoned honey of her own. Back to the future, Jules wakes up, Caleb's gone, and so's the sword.
Alan barges into the lab, asks for Sarah, and is about to barge out in search of her when Kyle lamely stops him with nervous questions about Arctic Biosystems and Paris. The subtlety of Kyle's spycraft could use some work -- like, all the work -- and Alan's like, who do you really work for? Kyle's non-answer gets him thrown through a plastic curtain and throttled, but while Alan's choking him out, Kyle's handcuffing Alan to a … bedpost? In a lab? "You're making a huge mistake," Kyle's told.
Agnes tells Michael about Sarah's super-healing as she prepares a syringe. She's like you, she tells Michael, injecting his eye with a solution that turns his silver eyes blue. He lied to them that there were no others like him, she complains -- he knew all along, didn't he? And why didn't he make Agnes like him too? Michael croons that she's always been his favorite "of all my daughters." Shudder. You just know he's going to kill her, and after burbling about a lack of trust, sho nuff he snaps her neck. Bye, Agnes. We'll miss how much you also hated Amy.