Ex Machina director Alex Garland's second sci-fi feature, Annihilation, has just arrived in theaters to rave reviews. Based on the novel of the same name by Jeff VenderMeer, Annihilation stars Natalie Portman as Lena, a scientist who ventures into a mysterious and highly dangerous phenomenon called the Shimmer, on a mission to find out what happened to her husband, Kane (played by Oscar Isaac) when he went on a previous expedition.
The events of Annihilation are not presented in chronological order; the film opens with Lena being interviewed after she has returned from the Shimmer. She is asked individually about each of her teammates, and says that each one is either dead or missing. The following timeline of events reorganizes the film to present the story in chronological order, from before Lena enters the Shimmer all the way to the film's conclusion.
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Before the Shimmer
If the story that Lena tells is true, Lena and Kane meet during her time in the army. They get married, and she becomes a professor of cellular biology at Johns Hopkins. Kane, however, continues working as a soldier, and goes on long, classified missions. It is unclear when Kane begins working for the Southern Reach in particular.
Lena cheats on Kane with Daniel, a married colleague, which Daniel attributes to Kane's absence and inability to connect with Lena on an intellectual level. When Lena ends her affair with Daniel, she tells him that Kane knows about the affair; presumably this means that she ended the affair before Kane leaves for the Shimmer. Kane is forced to leave for the Shimmer a day early, and his morose goodbye could be related to Lena cheating on him or the possibility that he may never return.
Kane in the Shimmer
Kane enters the Shimmer around a year before Lena does, and while not all of the parts of his story are clear, it's possible to piece together what happened to him. While in the Shimmer, Kane and his team camp at the abandoned site of the original Southern Reach base. They take turns scouting the parameter. The team members become aware that the Shimmer is affecting their minds and bodies, and they record footage of Kane cutting open one of his team mates to show how his intestines are snaking and moving inside of him. The teammate appears to have flowered into a hybrid human-plant. Kane and any remaining team mates leave the video recording in a plastic bag for the people who come after them.
Kane eventually makes it to the Lighthouse, and there meets his doppelganger. Inside of the Lighthouse, he has his doppelganger film him, and tells the doppelganger to find Lena. Then, Kane kills himself using a grenade.
"Kane" Returns
The film's first flashback shows Lena around one year after Kane's mission into the Southern Reach. Daniel invites her to a barbecue, which she declines, and he tells her that being social isn't disrespectful to Kane's memory. Because the scene happens early in the film, the viewer may not realize that Daniel and Lena previously had an affair, creating an additional layer of tension between them.
At home, Kane's doppelganger returns to find Lena. She is elated, and then concerned when he does not seem to be acting like himself. He struggles with words, and then begins bleeding from his mouth. The Southern Reach intercepts Lena and "Kane" in an ambulance, and "Kane" is stabilized at the Southern Reach facility.
Lena is interrogated by Dr. Ventress, a psychologist, for information about Kane, who is the first person to return from the Shimmer - or at least, so they think. Lena stays at the facility to watch over Kane, and she learns from Cass Sheppard, Anya Thorensen, and Josie Radek that they are preparing to enter into the Shimmer to go to the Lighthouse that is "ground zero" of the strange transformations. Lena convinces Ventress to allow her to come on the team, telling Ventress that she "owes" Kane - it's not explicitly stated what Lena means, but she could feel that her affair drove Kane away. Lena does not tell Sheppard, Thorensen, or Radek that she is Kane's wife.
Lena in the Shimmer
The team enters the Shimmer and then blacks out. They do not remember setting up camp or how they spent the first four days in the Shimmer, even though their rations are lower. They discover that most of their technology, from the radios to compasses, doesn't work. Despite these setbacks, they begin to work towards the lighthouse. The team arrive at a boathouse that is covered with many seemingly different flowers growing from the same vine. They encounter their first mutated creature: a crocodile that appears to have the teeth of a shark. The crocodile attacks Radek, but Lena kills it.
Taking the boats from the boathouse, the team makes their way to the former base of the Southern Reach, now overgrown with plants and deserted. Inside of the base, they discover a video tape in a plastic bag that is seemingly addressed to them. They watch the tape in horror as Kane cuts open his team mate and holds his moving guts. They find a hybrid corpse-plant that shares some similarities with the man that Kane cut open. The entire team, and especially Radek, is unnerved by the video, and they argue over whether or not the previous team went crazy or mutated.
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Team Member Deaths
That night, while on watch, Ventress tells Lena that it is a good thing that she did not tell the team that Kane was her husband, as they wouldn't know what to think of her after the video. They hear a noise, and as Sheppard comes out to join them, a mutated bear grabs her and drags her away. Because of the dark, only Lena, with night-vision goggles, sees the bear. The next day, Thorensen and Radek want to leave and Ventress wants to go forward; Lena convinces Thorensen and Radek to continue onward toward the coast and Lighthouse. The next day, Lena finds Sheppard's body and confirms that she is dead.
The team comes upon some flowering trees that are in the shape of human beings. Radek suggests that the Shimmer is a prism, but not just of light - the Shimmer is actively refracting and changing everything, including the cellular and DNA make-up of plants, animals, and humans.
Thorensen, increasingly aware of changes to her own body and mind, becomes paranoid and ties up her teammates. She discovers that Kane is Lena's husband, and rambles that Lena is a liar and untrustworthy. Thorensen is about to hurt Lena when she hears what sounds like Sheppard screaming. She assumes that Lena lied about Sheppard being dead, and runs to save her. It turns out that mutated bear that killed Sheppard, however, mimics the sound of Sheppard's screams, killing Thorensen.
In the morning, Ventress leaves Lena and Radek to continue towards the Lighthouse. Radek transforms into a hybrid human-tree, leaving Lena to follow Ventress to the Lighthouse.
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The Lighthouse
Lena approaches the Lighthouse to discover that it is surrounded by crystallized trees and features an arrangement of seemingly human bones outside. Inside, she finds an immolated human body and a video camera. She plays the tape from the video camera and sees her husband speaking to someone off screen. He instructs the person to "find Lena", and kills himself by grenade. Then, Kane's doppelganger enters the frame, and Lena learns that her husband has died.
Lena climbs into a hole in the floor of the Lighthouse into a cave with shifting walls. Ventress (or a copy of Ventress, since she is first shown without eyes) is sitting in the cave, reveals to Lena that she can feel something inside her taking over and changing her, and that this force will annihilate everything. Ventress is consumed by the force becoming a constantly shifting, shapeless form. A drop of Lena's blood flies into the form, and it begins to take human form.
Lena tries to flee, but the human form follows and mimics her. As she fights back, the form also attacks her. In a desperate attempt to escape, she tricks the doppelganger into holding a grenade after she's removed the pin. She runs for the door and escapes as the doppelganger explodes and the Lighthouse catches fire. Lena watches the Lighthouse burn and the crystallized trees crumble around her.
Lena has escaped... or so it seems.
After the Shimmer
In the final chronological scenes of the film, it is unclear if Lena or her doppelganger "Lena" have returned to Southern Reach. Lomax interrogates her - the opening moments of the film - and Lena or "Lena" answers questions the best that she can, recounting the entirety of her time in the Shimmer. Lomax reveals that the Shimmer collapsed and "Kane" regained consciousness, and Lena or "Lena" goes to see him. She asks "Kane" if he is the real Kane, and he responses that he doesn't think so. He asks her if she is Lena, and she doesn't respond. Instead, she embraces him, and their eyes change colors, illustrating that the Shimmer lives in both of them.
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