Acceptance, by Jeff Vandermeer, is the third book in the Southern Reach Trilogy. The story opens with Saul Evans, a lighthouse keeper, going about his daily rounds. After having a personal crisis about his true gender orientation, he left his job as a preacher in the North and traveled to the far South. Once there, he had taken a job as a lighthouse keeper. His lover, Charlie, works on a fishing boat in the nearby town.

Henry and Suzanne, two researchers, visit the lighthouse often. Their visits irritate Saul. He is certain that they were the ones who damaged the lens on the beacon a few days earlier. Gloria, a 10 year-old local girl, comes by to see him almost every day. She helps him do chores or plays by the water's edge.

The focus shifts to the present day and Ghost Bird. Ghost Bird and Control are main characters who jumped through a portal and landed in Area X at the end of the last book. Now they are walking toward the island. They head there because they believe that the biologist and her husband may have found a way to exist there. She can tell that Control is showing symptoms of an infection. He is feverish and paranoid. She feels protective of him. That amazes her.

In order to escape Southern Reach and her work, the director (Cynthia) routinely goes to Chippers Lounge and pretends to be a long haul trucker so people will treat her like one of the regulars. While she is sitting and drinking, she begins to think back to when she had first asked Whitby to help her pull off an unsanctioned crossing into Area X. He had readily agreed. However, once they returned, poor Whitby had never been the same. It was then that she realized that Area X infected people with a 'brightness'. Even now, she knows that she is fighting off the infection.

Meanwhile, in the past, Saul is cleaning up in the area around the base of the lighthouse. He sees some shards of glass and a beautiful white flower growing near it. He goes to investigate and gets a sliver of the glass embedded in his finger. He thinks nothing of it and goes about his routine chores.

Control lies there in the dark with Ghost Bird's arms around him. He is thinking about jumping through the portal to come to Area X. They almost drowned. He feels that he is changing, and he does not know if he is strong enough to fight it. He has so many questions. His greatest fear is that he will never know the answers. He sometimes shoves his hand into his pocket to find the carved chess piece that his father had made for him so many years before.

Back at Chipper's Lounge, Cynthia sips on her drink and thinks about the last time she saw Saul. She had been leaving to stay with her father, someone she personally detested, and Saul had asked her not to forget him. She suddenly misses the old man terribly. She had not told Whitby that the burned out cottage that they had gone through had been her childhood home.

Meanwhile, Saul feels ill. He agrees to see a doctor after Gloria shows concern. Not wanting to worry the child, he goes to see a doctor in town. The doctor tells him it is the flu, but Saul feels that he is wrong. He is disconnecting from other people, and he feels numb.

Ghost Bird spots a floating bag in the sky and immediately throws Control to the ground and covers him with her own body. He asks her what is going on, and she explains that it is scanning for anomalies. He is the anomaly. A storm comes but she shelters him from it most of the night. In the morning, they start walking for the island. At the edge of the mainland, they can see the island and find a rowboat stashed nearby. They hope that the biologist and her husband might have made it to the island and have found a way to survive in Area X. They get in the boat and push away from shore.

The Director thinks about when she had confronted Lowry about Southern Reach. He had invited her up to his secret facility where to her amazement she found that he had recreated Area X in a large concealed area. She learned that Lowry was afraid of Area X and has always seen it as the enemy ever since he returned from Expedition 1. Cynthia is appalled that he would consider Area X an enemy.

Control and Ghost Bird spend the night on the island. When they wake up, there is someone staring down at them. It is Grace, the former assistant director. She tells them that she has been there for two years after escaping Southern Reach's breach. This confuses them as they have just come into Area X after Southern Reach's demise. The distortion of time is evident.

Grace gives them the Biologist's journal when they ask if she has seen the biologist. They read that the biologist, upon escaping from her incarceration had come to Area X looking for her husband. She chronicles the survival techniques that she used, samples of the area that she took, and her observations about the 'brightness' in her. She writes that in order to keep the change at arm's length, she inflicts pain on herself every other day, something that Grace, too, has adopted. The pain makes her remain human. She is convinced that the owl is her husband who has undergone a transformation. It does not act like a typical owl and brings her food regularly, opting to roost near her at night. She indicates at the end of her journal that the owl has died and that she has been there for many years without hope of meeting up with any other human being. She says that she will no longer hurt herself and will allow the change to occur. The journal ends.

Saul wakes in the middle of the night and runs up into the lantern room of the lighthouse. He finds Henry, Suzanne, and another woman up there. He threatens them all with a hand ax and makes them leave. He learns that Henry made the hole in the lens because he believed that he was letting out a paranormal anomaly.

The Biologist has changed into a large amorphous creature of a thousand eyes. She breaks down the door to the old lighthouse where Control, Grace, and Ghost Bird have been staying the night. Control has some of the creature's body wash over him and he begins hallucinating. The next morning the Biologist is gone, but Ghost Bird says that they reestablished their connection, that no matter where the biologist is now, Ghost Bird will know and they can avoid her.

Meanwhile, Saul is feeling horrible. He knows that he is most likely not going to make it until Charlie returns from his fishing trip. They have had their last meal together at the diner, and then Charlie had left Saul to continue drinking and listening to a band. Saul has a psychotic break and thinks that he sees all sorts of horrific images and actions by the people in the diner. He drives the truck as far as he can. Then, he gets out and stumbles into the woods.

Ghost Bird, Grace, and Control go to the tunnel. Ghost Bird says that she and Control will go into the tunnel, while Grace stands at the top guarding the entrance. They go into the tunnel, and Ghost Bird stops in front of the Crawler. She gently embraces the light that circles his head. Control walks past her to where he has seen a large white flower surrounded in a brilliant white light. Setting the carving from his father on the last step, he steps into the white light and is gone. Grace, fearing the worst, comes down the stairs and sees Ghost Bird with the light. Grace panics and shoots her. Ghost Bird is unharmed. Grace leaves and goes back up the stairs.

Meanwhile, in the past, Saul has pulled himself back into his truck and has managed to make it back to the lighthouse. He climbs the stairs and finds Henry there. They fight, and both men go over the railing and land on the ground. Both are unharmed. Saul gets up, confused. Henry gets up and walks to the top of the lighthouse, once more, and Saul can tell that he is communicating with something alien. He no longer cares. He gives in to the brightness in his chest.

The director sips another drink. It is the past, and she is a day away from Expedition 12. She is hopeful that the Biologist will help them discover some of the questions that plague them about Area X. In the end, the director knows that they have been terribly wrong about Area X and its purpose. They have been wrong about their place in the universe. She finishes her drink and leaves.