Matty, the protagonist, is a teenage boy who lives with his blind guardian called Seer in a village simply called "Village." The community is a utopian place where the selfless inhabitants help each other as much as possible; they even provide the constant stream of new arrivals with food, clothes, shelter, and education. They have changed Matty, who once was one of those refugees, from being "the fiercest of the fierce" to a decent young man.
Matty's town is surrounded by a mysterious forest, which seems to be alive and deadly. For example, it warns people by stinging them with twigs, and when the warnings are ignored and the forest is entered again, the intruder is killed. Matty, however, is able to go through the paths in the forest without being harmed by it, so the village leader tasks him with delivering messages to the other towns in the region. Therefore, Matty wishes that one day he will be a full member of the village when he receives what he feels should be his true name, "Messenger."
On one of his journeys, Matty also discovers his gift: He is able to heal a frog with a severed leg. Later, he uses this gift to revive a dog and her puppy, who he adopts and names Frolic. However, every time he uses the gift, his energy is drained, and he needs some time to recover.
Feeling that he is now old enough, Matty wants to desperately visit the mysterious Trade Mart, because he learned that the family of one of his friends got a Gaming Machine and he wonders how one can get these items. At the Trade Mart, however, Matty is surprised that nobody brought any tangible items to trade. Instead, the villagers seem to trade their self to receive immaterial goods. For example, the schoolteacher Mentor trades his personality for a better look to appeal to a woman he has been courting.
Due to these trades, the altruistic nature of Village changes. The villagers become increasingly selfish, culminating in a town meeting where they decide to build a wall and prevent new refugees from entering.
Seer fears that his daughter Kira, who dwells in a village on the other side of Forest, will not be able to live with him as she promised. Therefore, he sends Matty through the forest to get her, while Leader asks him to post notices all over the forest informing people that nobody is allowed to enter Village any longer.
While going through the forest with Frolic, Matty notices that it is getting darker and more hostile toward him. However, he manages to get through and meet Kira. The young woman reveals her gift to him, which is her ability to foresee the future by stitching. Kira has a stiff leg, so Matty tells her that he would be able to heal it so that she could move to the dangerous forest more quickly. However, Kira declines his offer, saying that she would lose her identity and become someone else, which she does not want.
On the way back, the two are attacked continuously by Forest's flora and fauna. They barely make it to the middle when they run out of strength. At the same time, Leader, with his gift of seeing beyond, has started to fight through the forest as well to rescue them. However, he is soon trapped by a vine and unable to move forward.
Just when it seems like there is no escaping the vicious forest, Matty uses his gift to lie down and embrace the earth, thus healing the forest and everything in it, including Kira and Leader. However, this process drains him completely. He has sacrificed his life to reverse the effect of the dark forces. The villagers stop building the wall, and their previous personalities are restored. In the end, Leader awards Matty his true name: Healer.