Florida Stalker Lena is a biology professor, ex-soldier, and wife of Kane, a soldier, who is regularly away from home on secret missions. She cheats on him; he finds out, and volunteers for a mission that no one has ever returned from. He enters the Shimmer - a weird alien area, much like the Zone in Tarkovsky's Stalker. He returns after a year, but something is not right, so Lena also volunteers, and enters the Shimmer with a five-member all girl team.
Annihilation is a mind bending experience. If you get the vibe, you will probably want to watch it one more time. But you may end up hating it, because it is not the kind of story you typically expect from a sci-fi. There is a mysterious, alien area in the movie, depicted brilliantly using great pictures and CGI, but the story is centred on a journey inside our minds (again, just in case of the Stalker). The Shimmer, as it is explained in the movie, is a bit like a tumour: it reshuffles/mixes the structure of everything - crystals, genes, and even mental processes - and so speeds up change enormously. Why would one want to enter such a dangerous zone? Because it is part of our nature, Ventress, a psychologist explains. Most people have self-destructive tendencies: if something is fine with our lives, we cannot be happy with it, we want to change it.
But while we can never be fully satisfied with what we have, and regularly look for something new - a change, we are also frightened of change. Potentially, because we feel that if we change, we are no longer ourselves. As Ventress puts it at the end of the movie, "Our bodies and our minds will be fragmented into their smallest parts until... not one part remains - annihilation". So that would be my read on the movie: our constant thirst for, and fear of change, and the tension this constant struggle creates in our minds.
In the very last scene the couple meet again. "Are you Kane?" she asks; "I don't think so" he answers. "Are you Lena?" is the final line in the movie. She is probably not. They have changed, and this might help them to move on. Tarkovsky's Stalker is about ultimately everything staying as it was before, why Garland's Annihilation is about ultimate change. I am not sure which vision is actually closer to reality.