Since the book and the movie are essentially two different expeditions into Area X, Jeff Vandermeer's novel doesn't provide many answers for the ending of Alex Garland's adaptation of Annihilation.
But the director does include some clues into his mind-bending, dreamlike journey into The Shimmer. So, what happened at the end, when Natalie Portman's Lena reunites with Oscar Issac's Kane? What was with the interpretive dance? What was the glowing in her eye?
While the "event" in the book is never explained, the opening of the film shows a meteor hitting the lighthouse, which is the setting of the climax of the movie. It seems that whatever was on that meteor began altering the area around it—refracting time, space, genetics, etc.—to mimic and assimilate it into an alien being or organism. The animals and the plant-humans were all beings with their genetics scrambled or affected in some way inside The Shimmer.
So that leaves the final scene, where Lena encounters ground zero of the event. She comes across the psychologist deep within the lighthouse. You might have noticed that briefly the psychologist's eyes are covered up when Lena first meets her. This might hint that this was in fact a copy of the psychologist, as we saw throughout the Shimmer.
From there, Lena goes back to the top of the lighthouse where she does the dance with the blob being. This seems to be an underdeveloped copy of Lena, as whatever it is inside The Shimmer attempts to recreate her genetic structure. We're watching it learn and adapt. In the video inside the Lighthouse, we see Kane (who has lost his mind inside The Shimmer), kill himself—convinced to do so by his own copy. Lena, however, does the opposite, handing a less-evolved copy of herself the incendiary grenade. With everything inside The Shimmer connected, this kills all the linked organisms.
At the end, we see the actual Lena, but one who has already been greatly changed by The Shimmer. Notice the tattoo on her arm and the glow in her eye. Some part of the being remains inside Lena, and Kane is actually just a copy of the real Kane.
I've seen a few other explanations, like this one that's far more scientific from Reddit:
So from what I got from it the movie is making a point about our human nature. We started out from a single cell, a singularly, and from there continued to evolve and change. The scientists (and Lena) go through this progression backwards: the walk into a world that is in constant evolution, and as Lena approaches the lighthouse everything begins to become one—then she finds the singularity. It’s almost like the history of the universe in reverse—but this singularity envelops humanity’s nature with it. And the nature it envelopes is our self destructive nature. Dr. V mentions that our self destructive nature is a part of our DNA, and we see how this nature manifests in Lena’s life through her history of cheating on her husband. As the scientists start to near the singularity they start to reflect their self destructive nature—threats to kill each other, the physicist (who we know has been having self destructive thoughts about herself) is willing to become plant-like and lose her original form.
When Lena enters the lighthouse she sees her husband in the video, but this is actually the singularity that took his likeness and his self destructive nature—his willingness to kill himself shows this nature. The husband that is behind the camera is his real self, but constantly mutating like Lena explains earlier in the movie when she says her cells are constantly changing. When she finds Dr. V, Dr. V has given herself up to the singularity. Lena only gave it some of her blood, but it was able to take some of her likeness. Once it touches her it takes her form, including her human nature- self destruction, annihilation.
The next part I’d have to watch again, I can’t tell if the singularity was trying to kill itself or have Lena kill herself. Regardless, the singularity lights on fire and again reflects humanity by destroying. Lena escapes but, like her husband, is changed by entering the shimmer. Her dividing cells were completely changing in likeness, and even though she’s out of the shimmer she’s physically a very different person.
That's pretty good, too!
It's clear there are no solid "answers" to this movie. This is one that was intended to start a discussion about humanity, biological origins, and the mysteries of impending ecological disaster. That's likely why director Alex Garland strayed so far from the book itself. This is a concept that deserves to remain unexplained. And certainly, as people digest this bizarre film, there will be many more theories as to what happened inside The Shimmer.
