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Annihilation's Most Confusing Scenes Explained

Biological life is a dizzyingly complex idea. How do our cells know what to do to sustain the absurdly complex systems that comprise a human being? What causes them to malfunction? How many of them would have to be replaced until we no longer qualified as "ourselves"? Alex Garland's 2018 movie "Annihilation," adapted with some major differences from the novel by Jeff VanderMeer, uses a mysterious alien entity to ask all of these questions and many more to bizarre and unsettling heights. 

It's a psychedelic and strange investigation into a phenomenon called "the Shimmer" that's taken over an entire section of the American coast. A journey into the unknown becomes a story about madness, loyalty, and a Crosby, Stills, & Nash song.

Like Garland's other sci fi works "Ex Machina" and "Devs," "Annihilation" is content not to over-explain itself, and may take several viewings to really get a grasp of all that's going on. There are human-shaped plants, mysterious doppelgängers, several new animal species, and a deep sense of foreboding that overshadows everything. The movie is somewhere between a dream and a nightmare, and perhaps just as difficult to describe with words, but that won't stop us from trying. These are the most confusing scenes in "Annihilation," explained. 

So it was alien

It's not until the very end of "Annihilation" that we discover how thoroughly the characters in the movie are operating in the dark. The movie is framed by an interrogation scene where the officious Lomax (Benedict Wong) and a crowd of anonymous people wear hazmat suits and ask main character Lena (Natalie Portman) what happened to her in the Shimmer. The audience is given key information that the team of military scientists and contractors don't until Lena clued them in: A meteorite crashed into the lighthouse where the Shimmer began, which means that it's most likely extra-terrestrial in origin.

But unlike most movies about aliens, "Annihilation" doesn't present the entity responsible for the Shimmer as any recognizable life form or consciousness. As Dr. Ventress (Jennifer Jason Leigh) says, it's not clear what it wants or even if it wants. Even though Lena comes face to face with it, or at least a manifestation of it, Lomax puts it plainly: "You really have no idea what it was." 

If we ever make contact with alien life, it's very possible that it won't be humanoid or even be capable of communication as we understand it. The Shimmer is one of the most bizarrely unique depictions of first contact — implausible in its particulars yet plausible in its inexplicability.

Does Kane know about Lena's affair?

"Annihilation" doles out some important subtext in fleeting glimpses that potentially explains both Lena and her husband Kane's (Oscar Isaac) motivations to enter the Shimmer. The couple met in the military, but Lena left to study cellular biology while Kane stayed to go on frequent top-secret missions that he can't tell her about. Years of growing distance between them culminate in Lena having an affair with her colleague Daniel (David Gyasi) sometime before Kane leaves for the Shimmer. It's strongly implied that Kane knows about the affair, which influences his decision to go on a mission that no one else returns from.

The movie reveals this information as cryptically as everything else, indicating that the infidelity itself is less important than the physical and emotional distance that's already between them. Although Lena seems to confirm to Daniel that Kane knows in order to get Daniel to leave her house, when Kane is leaving for the mission to the Shimmer, his morose attitude could be simply because he knows he's unlikely to return. "Annihilation" asks us to consider how many secrets we can keep from one another until we're strangers to each other.

The passage of time

"Annihilation" has two noticeable time gaps that are never properly explained. After initially entering the Shimmer, Lena and the others awaken to find themselves about "three or four days" into their mission, but without any memories since entering the edge of the anomaly. The events we see in the movie appear to take place over another week and half, but when Lena is picked up by the Southern Reach after the Shimmer collapses, she's informed that she's been gone for four months. She has no explanation to offer Lomax, even for basic questions like "what did you eat?"

The Shimmer, as Josie (Tessa Thompson) helpfully theorizes, is a prism that refracts everything: It's not a huge leap to assume that "everything" includes time itself, in addition to the genetic code of all life in the area. If time moves more slowly inside the Shimmer, it could explain not just the gaps in the chronology of "Annihilation" but also the time it takes for the members of the expedition to get used to it. It could also be another reason it eventually drives everyone but Lena mad.

The terrifying ventriloquist bear

Although the mostly meditative and strange "Annihilation" isn't really what you'd call a horror movie, it takes a hard detour into the terrifying when a hybrid bear-like creature kills Cass (Tuva Novotny) and then returns to menace the rest of the group. Arguably one of the scariest movie monsters of all time, the bear creature doesn't just roar at our heroines, it somehow can speak with Cass's disembodied voice and screams "help me!" Of all of the strange things the movie depicts in the Shimmer, the bear with huge teeth and the voice of a dead woman is by far the most disturbing.

It's also key in our understanding of the refracting capabilities of the shimmer since organisms can blend with one another seemingly in real time. Josie theorizes that part of Cass' mind became part of the bear in the moment that she was killed, trapping her in constant terror and torment until Josie manages to shoot the creature dead. Thematically, the bear refracts the idea of cancer and makes it an external threat: Instead of being killed by part of yourself, in the Shimmer, you become part of what kills you.

Helplessly Hoping

One the best touches that sets "Annihilation" apart tonally from other moody sci fi movies is the recurring use of the song "Helplessly Hoping" by folk trio Crosby, Stills & Nash, which is used as a theme for Lena and Kane. The lyrics refer to a "he" that waits silently for a "she," who never opens up to him, and he can't decide whether to run away from her or not.

Lena and Kane's marriage is shrouded in secrecy and for some, it's one of the more confusing elements of the film. Does Kane know about the affair? Are they doomed to keep drifting apart anyway? Kane and Lena certainly have chemistry and inspire deep happiness in one another at times. But the more they keep from each another, they more "confusion has its cost," as the song goes.

The refrain of "Helplessly Hoping" sums up Kane and Lena's problems with a clean bit of wordplay and can clarify some of the ambiguity around their relationship. They're wildly different individuals ("They are one person"), who are drifting apart ("They are two alone"), but still hoping to maintain the relationship itself, which they've been building for years ("They are three together"). 

They're both radically transformed by the Shimmer in the end and are reunited, so hopefully they can work it out ("They are for each other"). While you couldn't really say "Annihilation" has one of the best movie soundtracks, it does get the most mileage possible out of its lone pop track.

What happened to Josie?

Talking to Lena about the Shimmer, Josie says "Ventress wants to face it. You want to fight it. But I don't want either of those things." She then walks away as plant material starts to grow out of her skin, and seemingly vanishes around a corner after Lena falls too far behind her. What happened to Josie? The implication is that Josie willingly transforms into another of the human-shaped plants that the team encountered. She embraces the Shimmer and becomes something new, retaining at least her "hox" genes that dictate an organism's shape.

In short, she becomes one with the plants. Josie is by far the most empathetic and understanding of the team: She's the first to grasp the information and DNA-refracting properties of the Shimmer. Josie's calm acceptance stands in stark contrast to Lena and Ventress' determination, as well as Cass and Anya's fear. 

Josie embraces the unknown because she knows firsthand that life outside the Shimmer is no picnic. Cass mentions that Josie has struggled with self-harm, and the plants actually begin to grow from the scars on her arms.

If you or anyone you know is having suicidal thoughts, please call the National Suicide Prevention Lifeline​ by dialing 988 or by calling 1-800-273-TALK (8255)​.

Lena's Ouroboros tattoo

In the interrogation scenes, Lena has a tattoo on her arm that is noticeably not there during her time in the Shimmer or beforehand. It's a tattoo of Ouroboros, an ancient symbol of a snake eating its own tail that represents the infinite circle of death and rebirth (via Britannica). It's a potent symbol for the themes of "Annihilation," which also deals with the unity of all life in an intricate and connected cycle of ending and beginning.

If you watch closely, you can spot the Ouroboros tattoo "jump" from person to person. It's at first glimpsed on the arm of one of the corpses that the team finds, then seen on Anya's arm, and eventually rides Lena's arm all the way out of the Shimmer. While normally, an Ouroboros is drawn in a circle, here it's been twisted into the symbol for infinity as well, driving home the endlessness of biological growth and decay all the more.

The bones outside the lighthouse

In one of the more gruesome sights of "Annihilation," nine skulls and a variety of other bones are arranged outside of the lighthouse, seen as Lena makes her final approach. In what is perhaps a final warning, it's likely that these are the bones of the remainder of Kane's original expedition to explore the Shimmer. The same person — perhaps Kane himself — who left the horrifying video "for those who come after" of the soldier's moving intestines may have wanted to ward off anyone who wasn't already driven mad by the Shimmer's other terrors.

Of course, given the reality-bending nature of the Shimmer, it might be jumping to conclusions to assume that they're human bones to begin with. The way they're arranged also mirrors the mysterious crystalline structures along the rest of the beach. The Shimmer is really just trying to set the eeriest mood possible.

Dancing with myself

When Lena asks Ventress why Kane would enter the Shimmer when no one had ever returned, Ventress cryptically points out that humanity is reckless by nature: "We smoke and drink, overeating, ruining good prospects, destroying beautiful marriages ... these are not subjective wills. The choice is an impulse, the self-destructive impulse etched in our genes." Perhaps because we're aware of the "fault" in our genes (as Lena calls it) that will cause us to age and die, we instinctively self-sabotage in a primal rebellion.

Lena gets a chance to work out her own self-destructive impulses quite literally at the end of "Annihilation," as she tricks her own Shimmer doppelgänger into holding a phosphorous grenade. Just as the Shimmer copy grows a version of her face, Lena watches it go up in flames. Poignantly, Lena only is able to get the upper hand by learning not to fight her "evil" twin, since it mirrors everything she does, but to engage with it in a sort of dance. It's a part of her that she must accept, even as she destroys it.

Of course, Natalie Portman is no stranger to dancing with shadowy doppelgängers in psychological thriller movies and she brilliantly brings those previously established talents to "Annihilation."

Why did the lighthouse burn down?

When Lena blows up her doppelgänger, the Shimmer completely destructs, which initially seems like a minor plot hole. After all, if the organic parts of the Shimmer in the lighthouse are that sensitive to phosphorous grenades, why didn't everything go up in flames when Kane blew himself up a year earlier? It's actually just a bit of coincidental timing, and the mystery of the Shimmer's collapse is related to the thing Lena has spent years of her life studying: cancer.

Dr. Ventress disappears into the Shimmer in a burst of light, from which a psychedelic "Mandelbulb" shape emerges that eventually became Lena's doppelgänger. It's such a weird scene that it's easy to forget that Ventress was dying of terminal cancer, so it's her cancer cells that disrupt whatever energy the Shimmer operates on. 

After the Shimmer incorporates these cancerous cells, they act as a sort of self-destruct code that take the entirety of the Shimmer down with it. So, Lena is treated to a spectacular display of fire and light, as the lighthouse and all of the structures on the beach destruct at once.

You aren't Kane, are you?

Although he has a southern accent we haven't heard before (perhaps "refracted" from one of his squad-mates), it's more or less clear that the real Kane is the one that self-immolates on the video in the lighthouse. The casual way he asks his Shimmer doppelgänger, "You ever see a phosphorous grenade go off?" implies he's familiar with this being. 

The Shimmer is filled with duos — we see various pairs of animals within it — and it seems to instinctively duplicate all life within its boundaries, while radically transforming it at the same time.

Memories presumably are duplicated along with form: The copy of Kane that returns to Lena remembers her and knows how to find their house. But even the Kane duplicate himself isn't sure of what's what: When Lena asks if he's really Kane, he merely says, "I don't think so." But doesn't a being that has Kane's memories and looks exactly like him sort of count? 

Before he died, the real Kane essentially relinquished the title: "I had a dream I was a man... People called me Kane, but now I'm not so sure." So, in the end, Lena gives this new Kane a hug, embracing the parts of her husband that still remain, as well as the alien form of the Shimmer.

Are you Lena?

When Shimmer Kane turns the tables on Lena and asks her if she's Lena, she doesn't have an answer for him. While we are reasonably sure that she didn't swap places with her Shimmer doppelgänger, as she hugs "Kane," her eyes shimmer with a tell-tale glow. As Lena sees under the microscope early on in the expedition, she's been changed by the Shimmer at the cellular level, so who's to say if she's still really "herself"? She and Kane's double hug in a tentative embrace, perhaps to live happily ever after as two people profoundly changed in different ways, who can now cross the previous distance between them.

Even though it's not entirely accurate, "Annihilation" toys with the common biological idea that our cells are all replaced every seven years or so (via Live Science). As posed by the paradox of the ship of Theseus (via The Collector), are we still the "original" version of ourselves if every part of us is new? Lena has a stranger's tattoo, eyes that glow, and a new husband that looks exactly like the old one but isn't technically him. 

If she isn't the old Lena as she once knew herself, maybe whoever she is now — Lena with parts of the Shimmer inside — will do. Every day we wake up with a new body, new memories, a new person— and so every day is the first day of a new life, until the last one.