Spoilers ahead for Legion "Chapter 13." After being absent for all of Season 2 to date, Amy Haller (Katie Aselton) finally returns to FX's superhero series in a huge — and hugely tragic — way. What happened to David's sister on Legion? The answer to that question is inextricably linked to the answer to the question of how Lenny came back to life. It turns out that giving David's best friend her body back came with a terrible price, one that has shattered whatever tentative alliance David and the Shadow King may have had.
Throughout the May 1 episode, "Chapter 13," as the resurrected Lenny is being interrogated at Division III by Clark, Ptonomy, and David in turn, the question that keeps popping up is: "Whose body is that?" Given that Lenny's own corporeal form was phased through a wall when Syd temporarily wielded David's powers in the series premiere (and given that it's been rotting in the ground for over a year since), the team is unsettled by the possibility that Amahl Farouk had given Lenny somebody else's body.
This theory gains weight when Ptonomy — he of the eidetic memory — incorrectly remembers the color of Lenny's eyes. Or rather, he correctly remembers what color they used to be: brown. But now they're blue. When he tries to peer into her memories, he also gets flashes of memories she shouldn't have: namely, a vision of Admiral Fukuyama and his Vermillion, which gives viewers their first terrifying glimpse of Fukuyama's real, insectoid face lurking underneath his wicker basket.
Eventually, the truth is revealed through a deceptive flashback. While the viewer is led to believe that Farouk has located his own body, it's revealed that his exhumation activities with Oliver aren't taking place in the present, but in the past; and the body being dug up is Lenny's, not Farouk's. Farouk takes a piece of flesh from Lenny's corpse and inserts it into a machine that Oliver stole during his incursion into Division III earlier in the season. The pair then follows a donut stand shaped like a submarine to an isolated house in the middle of the desert, where a familiar face is hiding out.
Sometime after the events of Season 1, it appears that Division III essentially put Amy Haller into witness protection, putting her in a remote location surrounded by guards. But those guards aren't enough to stop the Shadow King when he comes calling (in the form of Oliver), turning her boyfriend to dust and paralyzing her with his telekinetic powers. He then uses the DNA-loaded gun to transform Amy's body into Lenny's, resurrecting David's best friend by horrifically killing his sister — or so it appears.
Here's a thought: if you know your nemesis is one of the strongest mutants in the world, maybe it isn't the best idea to piss him off in the most personal and painful way possible? It seems like a bad idea for the Shadow King to break his truce with David by murdering Amy… but then again, maybe it's all just part of the supervillain's plan.
In the comics, David Haller's full powers weren't triggered until his stepfather was brutally murdered by terrorists in front of his eyes. Maybe the show is adapting some form of this origin story with a different family member, and Farouk is trying to coax out David's true potential for his own nefarious purposes. Regardless, it now makes sense why David would end up bashing Farouk's head in, as future-Syd warns David he will do when she visits him in the Orb.
Definitely the weirdest part of this whole turn of events — yes, even weirder than a DNA ray gun that shapeshifts bodies — is the recurring dream Amy had been having, which she describes to her boyfriend shortly before dying. In it, Amy appears to be inhabiting the mind of one of Fukuyama's Vermillion. Between that and the memory Ptonomy unearths of the Admiral, Amy appears to be sharing some sort of psychic link with the Division III leader. But why? And how? Up to this point, David's adopted sister had appeared to be entirely human. Maybe she was hiding a big secret, the true nature of which wouldn't be uncovered until her death.
Somehow, this tragic Legion development manages to raise more questions than it answers. But that's par for the course for this show.