Annihilation — both the book by Jeff VanderMeer and the film directed by Alex Garland — is the kind of story that offers more questions than answers, so it's no surprise that neither version is fulfilling in that regard. Just like the novel that inspired it, the film is at times incomprehensible, illogical, and hard to follow, although all intentionally so.
What the film is going for becomes even more apparent when it reveals its final twist in the last couple seconds. Audiences may be confused by the sudden reveal, which we talk about below, but you can see the signs from Annihilation's opening minutes if you know where to look.
SPOILER WARNING! MAJOR SPOILERS FOR ANNIHILATION SHIMMER BELOW...
The story of what happens in the Shimmer — an ever-expanding patch of land similar to the Bermuda Triangle where people go in and never come out — is told to the audience by protagonist Lena (Natalie Portman), who has just come back from an expedition into the unknown area. All of her colleagues are dead or missing and considering nobody comes back from the Shimmer, this is kind of a big deal. The only person to come back was her husband Kane (Oscar Isaac), but he's not himself. He doesn't remember anything, acts strangely, and soon falls into a coma. Lena's journey into the Shimmer is motivated by the promise of scientific discovery, but also by finding out what happened to Kane.
As the audience learns, it's not a happy ending. Her real husband died inside the Shimmer, so who or what came back out? Going even further, the final moments reveal that Lena also never made it back out. Whatever duplicated her husband has done the same to her and has been tricking the government officials at Area X this whole time.
We're cued into this by unnatural movement in her eyes, but there's also another sign, and this is the one that a lot of people may miss: a tattoo.
The tattoo is around from the beginning of the film. From far away it looks like the number eight, but on closer inspection it looks more like a snake. Like many other sci-fi properties — including the recent Netflix series Altered Carbon — Annihilation seems to be reimagining the Ouroboros, or a snake eating its own tail. The symbol usually represents the cyclical nature of life, or the theory of the "eternal return," a concept about how all life will occur and reoccur until the end of time. Considering what happens at the end of the film and the repeated idea that whatever is happening in the Shimmer isn't destroying life but is "creating something new," it's most likely the latter.
The symbol appears on a number of characters. The main one is Lena herself, which we can see as she's being interrogated by Lomax (Benedict Wong). It's quite large, taking up most of the left forearm, and is quite distinct. However, when we flash back to Lena's time in the Shimmer and even before that, there is no tattoo.
So she got it inside the Shimmer, but how? Well, remember when I mentioned that something took the place of her and Kane when they reappeared in the outside world? In the film's climax, Lena enters the lighthouse — the focal point of the Shimmer — and encounters what can only be described as a rolling mass of glitch art that forms into a humanoid, faceless being. Lena tries to run, but is confounded by how it doesn't seem to be directly attacking her, but mimicking her every move. Lena eventually makes physical contact with the creature (named in the credits as Humanoid), but that's when it morphs into her double, complete with the mysterious tattoo. You can see it on the creature's forearm before Lena lights it on fire.
So at some point, the Humanoid was able to switch places with Lena, although when is a little unclear, since one of them was, you know, burned alive. The Shimmer works in mysterious ways and sometimes without logic, so it could've happened at any point.
Other characters directly affected by happenings in the Shimmer also sport the tattoo. When the group stumbles upon a video camera with footage of what happened with Kane's expedition, they see the disturbing flaying of another soldier. Our focus is on his stomach, which is cut open to reveal moving insides, but if you know where to look, you'll find the same Ouroboros tattoo on his arm. This is the guy who later becomes some nausea-inducing art on the wall of a swimming pool.
Anya (Gina Rodriguez), is in the current group. It's revealed that she's partially on the mission to escape her past as a drug addict, so when she starts questioning everything she sees, it's personal horror made real. This eventually leads to a meltdown where she says she saw her flesh moving, and a sequence where she ties up the other members of the group to get answers. Anya was often seen without her jacket on, but this is the first time we see the tattoo on her arm as well. This is also just before she dies. Does this mean that she was replaced or that she was merely affected by the Shimmer?
The forearm is an important body part in Annihilation, beyond the placement of the tattoo. When Lena first notices a bruise after a scrape with a mutated crocodile, it's forming on her forearm. She later takes blood samples from it only to find that whatever is in the Shimmer has started to affect her DNA.
Later, Lena sits by Josie (Tessa Thompson) following the traumatic night of Anya's breakdown. It had been previously stated that Josie self-harmed and wore long sleeves to cover up the scars, so when Lena gets a look at Josie's forearm, this is the first time the audience gets to see them as well. No tattoo here, but there's something else. At first, it just looks like there's a piece of grass that Josie's wiping off, but in the next few shots, we see it spread. She walks into the trees, becoming covered in more branches and leaves before vanishing. Lena follows her into the woods only to come across a clearing filled with the same people-shaped plants. We are left to assume that Josie was subsumed by whatever affected the village's previous residents.
It's possible the forearm has some metaphorical relevance, but it also might've been a trick by the filmmakers to draw attention to that part of the body so the audience could notice it on other characters. And for the eagle-eyed viewers that did notice it, they had the proof for the twist ending at minute one.
Were there any other appearances we missed? Do we have to watch the film again? Probably.