Maya lives in a small medical-research town on Vancouver Island. How small? You can’t find it on the map. It has less than two-hundred people, and her school has only sixty-eight students—for every grade from kindergarten to twelve.
Now, strange things are happening in this claustrophobic town, and Maya’s determined to get to the bottom of them. First, the captain of the swim team drowns mysteriously in the middle of a calm lake. A year later, mountain lions start appearing around Maya’s home, and they won’t go away. Her best friend, Daniel, starts experiencing “bad vibes” about certain people and things. It doesn’t help that the new bad boy in town, Rafe, has a dangerous secret—and he’s interested in one special part of Maya’s anatomy: Her paw-print birthmark.
The setting for the Gathering is a small medical-research town called Salmon Creek on Vancouver Island. Salmon Creek was built by the St. Cloud Cabal, the owners of the town and surrounding park, for their employees. Maya is the adopted daughter of the park ranger. The events actually start a year before with death of Maya's friend, Serena, the captain of Salmon Creek High swim team, drowned in the lake, and Maya is guilt ridden for not being able to save her friend.
A year later, Maya is getting ready to celebrate her sweet 16. She wants to tattoo her birthmark—a paw-print shape on her hip. She doesn't want it altered in any way, though; she just wants to make it more noticeable. However, she doesn't get it because the tattoo artist's aunt insults her by calling her a witch in Navajo. She invites Rafe, a new bad-boy at school, to her birthday party at Daniel's house. At the party, the teens have a competition on Maya's new rock wall: if she can beat all the guys, they have to add more footholds, but if she loses to even one guy, she has to kiss him.
After she defeats all the contestants, Rafe shows up. He challenges Maya individually, and beats her. He doesn't kiss her, though, promising to claim his prize without prying eyes. Later, Maya and Rafe start going out. One day, when Maya was going over to his house for dinner with him and his childish older sister, Annie, she is attacked by someone looking for Rafe. She sees Annie transform from a cougar into herself.
Rafe tells her that skinwalkers are people with special abilities including being able to shift into mountain lions or bears and the ability to heal and communicate with other animals. He says that Maya, Annie, and himself are skinwalkers, that they carry their animal traits with them even in human form. This explains Maya's enhanced hearing and night vision as well as her amazing skill of rehabilitating injured and sick animals. Maya makes the connection between her paw-shaped birthmark and the fact that she is skinwalker. Rafe confirms this idea, saying that paw-print birthmarks indicate skinwalkers and that he and Annie both have them.
He also explains that skinwalkers had been extinct until an experiment to bring them back was enacted. He says that their birth mothers were selected to be part of this experiment because of their Native American DNA, but they didn't realize what was going on. Rafe thinks that Maya's biological mother learned the truth about the experiment, which would explain why she abandoned Maya when she was a baby. Maya also learns she may have a twin brother from whom she was separated at birth. Rafe explains that skinwalkers can't control when they shift and points out the symptoms that occur in a skinwalker before they shift, Maya realizes that she is going through these symptoms and may shift soon. Maya dumps Rafe after thinking that he dated her only because of her being a skinwalker, however, Rafe truly does have feelings for her.That same night, Annie disappeared while she was still in cougar form and her location is unknown by all characters. Rafe knows that Annie often runs off after she shifts, but is worried for her safety, especially when the forest catches fire. Maya, Daniel, and Rafe are in the forest during the fire, and start to run away when they see people. Daniel's asks Rafe and Maya to lay low because his special danger sense is tingling. They listen in on the people's conversation, and figure out that this group of people set the forest on fire in order to distract the town. The people would then break into the St. Clouds labs in order to steal the secrets housed there. The book ends after Maya, Daniel, Nicole, and an unconscious Rafe escape in a helicopter and report what they overheard to town officials.