The mystery of the Southern Reach trilogy isn't something that can be covered with one book. Annihilation and Authority were both intriguing books, for different reasons, and Acceptance takes the main ideas of both and incorporates them into a subtle, sort-of conclusion that leaves many questions unanswered, but doesn't leave the reader feeling like he missed out on a good story. But because the books are so dependent on one another, it's next to impossible to discuss Acceptance without spoiling not just this book, but the entire series. So stop now if you don't want to know what happens next.
Annihilation was narrated by a nameless biologist, who returned from Area X in Authority as a different person, a copy of her original self, and took on the name Ghost Bird. The person who takes the biggest interest in Ghost Bird is the current Assistant Director of the Southern Reach, a man who has a real name, but chooses to go by the name of Control. The missing director of the Southern Reach, who Control and Ghost Bird choose to retrieve from Area X, is mostly referred to as "The Director" (and, oddly enough, referred to in the second person in her chapters in this volume), and goes by the name Cynthia, even though her real name is revealed to be Gloria. So names -- or, more specifically, the lack of them -- are important in this series, as the individuals' anonymity becomes a key player in the series.
Like the main characters, Area X -- the part of the coastal United States that was regressively transformed into a primitive wilderness that's become hostile to human visitors -- isn't explicitly defined with a name. It feels like it's located in Florida, but it's never explicitly stated in the book. It's a foreign, alien land that either transforms, kills, or duplicates the human visitors that enter in hopes of finding answers. Area X holds on to its secrets well, enough so that even by the end of Acceptance, we still don't know where it came from.
There are definitely hints. It might be a portal to a duplicate, primitive version of Earth. It might be something controlled by aliens as part of a curious experiment. It might be an ancient life form accidentally let loose on an unsuspecting public. Whatever it is, it's expanding; by the start of this book in the series, Area X has engulfed the organization that was tasked with unearthing its secrets.
The thing is, it doesn't matter what Area X is or where it came from. What's important is that it causes disorientation to those who come in contact with it. We see a glimpse of what life was like along the Forgotten Coast before Area X took it over, and we get some clues that may point us in the direction of its origins. But like the ambiguity that the characters have regarding their own questions, we don't ever know for sure.
Overall, the story could be seen as an environmental parable, where the world decides to take itself back from humans, but that oversimplifies the texture and atmosphere of the novels. It feels heftier and more substantial than just a mere parable, but it's hard not to read a story as dense and incomprehensible as this (as in answers, not story) without trying to add your own context to it all. As an example, Acceptance has one named character who features as a point of view in the story, and it's hard not to attach importance to him, since everyone else chooses to remain anonymous through their own pseudonyms. It seems to be an important point, but I'm not sure if I could tell you what that point is. It could be something as simple as that the character exists before Area X takes over, but I also feel like it's more significant than that.
These novels feel like smaller parts of a larger story, and honestly, I can see how all three novels could be published under one cover and still be successful. To that point, I would recommend anyone interested in this series do just that. Binge-reading the books back-to-back seems like the best way to approach the series. In fact, having finished them, I wonder if I will be re-reading these that way at some point in the future.