Miranda, the seventeen-year-old daughter of scientists Kate and Cornelius Gregory, lives in the Domed City of San Diego in the year 2103. Her job in the environmentally controlled city is to care for the Last Tree, a dying eucalyptus. While on a visit to The Archives (a virtual library) to study the life of her famous environmentalist great-grandmother Gabrielle Leigh, Miranda travels through The Portal and somehow begins to materialize in the twentieth century. She follows Gabrielle from her native San Diego to Oregon, where Gabrielle meets sawmill owner Patrick McAfee. As the environmentalist and logger join hands, invisible Miranda forms a triangle with them and actually feels their hands beneath her own.

Patrick and Gabrielle begin to fall in love, and still-invisible Miranda follows them to their first dinner date at the Pine Hill Inn, where she tastes real coffee and chocolate for the first time (in Miranda's century, all food is made from recycled algae).

Miranda returns to her Homeplex under the Dome to tell her mother and father about her adventures in the twentieth century. They call a meeting of The Gathering, a group of scientists who want to reintroduce wilderness and remove the Dome. The Gathering encourages Miranda to continue her journeys--but to be careful and take the necessary equipment. Miranda returns to Oregon--a couple of years after the dinner at The Pine Hill Inn. She finds Gabrielle and Patrick married, and Gabrielle pregnant with their first child. She watches the young couple kiss goodbye, feeling certain that Gabrielle senses her presence and is trying to tell her something. Then she jumps in Patrick's truck and rides up the mountain to the logging site, where a battle between the loggers and radical environmentalists erupts. Patrick is shot, and Miranda grabs her medical kit and rushes to his side.

Miranda cannot save Patrick, but she tells him about his unborn child and the future. He sees her and replies before he dies. Miranda rides back to town with Patrick's body, witnesses his funeral, and follows Gabrielle as she leaves town and moves into a remote mountain cabin, where she can grieve in peace. During a storm when the mountain roads are impassible, Gabrielle goes into labor. The now half-visible Miranda helps bring her own grandmother into the world. As baby Julia grows, Miranda becomes completely visible in the twentieth century. Miranda and Gabrielle (with little Julia) hike among the evergreens and plan how to save trees for the future.

A group called Force One, made up of people who don't want to reintroduce wilderness or destroy the Dome, send a Spy to Gabrielle's twentieth-century cabin. Miranda sees the Spy hiding in the trees one night and returns to her Homeplex. Miranda's parents and a young scientist named Michael, who is attracted to Miranda, promise to help catch the Spy. But before they can make any plans, with the Enforcers (local police) close behind, Kate, Cornelius, Michael, and Miranda must gather their equipment and leave the Dome. They follow abandoned drainage tunnels under the Dome and emerge at old Miramar Lake. For the first time in her world, Miranda sees a sunset. From outside the Dome, without using a Portal, Miranda returns once more to the twentieth century. Will she help Gabrielle save trees for the future, like Noah saved animals in the Ark? Will Force One face The Gatherers in one final confrontation? What will happen to Gabrielle and her descendants? Will the future continue to be enclosed in Domes? To find out, read the book!