After helping Chip and Alex survive fifteenth-century London, Jonah and Katherine are summoned to help another missing child, Andrea, face her fate. Andrea is really Virginia Dare, from the lost colony of Roanoke. Jonah and Katherine are confident in their ability to help Andrea fix history, but when their journey goes dangerously awry, they realize that they may be in over their heads: They’ve landed in the wrong time period, and Andrea doesn’t seem that interested in leaving the past. Even worse, it appears that someone has deliberately sabotaged their mission...
The book starts where the last left off. Jonah, Katherine, and Andrea are going to be sent back in time to Andrea's time. JB is going to give them a briefing, but his projectionist, Sam, says to brief them after they get there. He does tell them that Andrea is Virginia Dare, the first English child born in the colonies. When they arrive, the Elucidator is gone. Andrea blames Jonah, but Jonah figures out that Andrea was the one who lost it. Deliberately. Andrea begins to tell them why. She says that the night before they left to the 1600s, a man came to her and said that if she did what he said, and plugged in the numbers he gave her, she would be able to do the one thing she always wanted to do, save her parents. Her parents had died in June one year before. Katherine explains that she could not go back to that time and relive it, which is the paradox of doubles. They go through a series of events including saving John White, Andrea's grandfather. They also save Antonio and Brendan, two boys who were to make great artwork. They have tracers which they mix with, implying that they are time travelers. Eventually, a man who calls himself Second gives them food and later on, a jar of paint for John White. Jonah gets furious with Second's "gifts" and says that they all should try to do the opposite of whatever they are going do because it must've been what Second would have wanted. Later on, Jonah follows the tracer boys and finds a canoe and they all follow the tracer boys. In the middle of paddling, Jonah is hit by two boys named Brendan and Antonio in mid-air and falls into the water. He is rescued and sleeps throughout the day. When he wakes up, he finds himself on an island with Andrea, Katherine, John White, Dare, and Brendan and Antonio. Katherine then explains that Second came to Brendan's and Antonio's rooms and sent them here and that they are the real versions of the tracer boys. The boys learn to fish and set up a campfire by being with their tracers and on the next day they head to Croatoan Island. When they arrive, they find that there are dead skeletons everywhere and the reason why nobody went to Croatoan Island is because the tracer boys think that the "evil spirits" of the dead haunt them because of their killings. The tracer boys wake up the tracer version of John White and show him the island. Then the tracer boys say that they hear the sounds of the evil spirit so they head back to the canoe, but Dare runs off into the woods and Jonah chases Dare into the woods and finds Virginia Dare's tracer. He calls Andrea to mix with her tracer, but then while Andrea is within her tracer, she says that Virginia Dare won't come out of the woods until the tracer boys leave. Andrea becomes furious, and suddenly the tracer is inside Andrea. Now Andrea, Brendan, and Antonio get to control what happens. They wake up John White and Virginia Dare meets her grandfather. A man comes up behind Jonah and Katherine and says that what just happened is a second chance in history. The man says he calls himself Second because he gives people second chances. He reveals that his real name was Sam Chase, causing Jonah to figure out that Second/Sam was JB's projectionist. Second/Sam explains that he sent them to Roanoke Island to rescue John White and bring him to Virginia Dare, when actually they were supposed to go the moment where Virginia Dare buries the bones to honor the people of Croatoan Island. Then it actually means that Second/Sam really didn't "Sabotage" their mission, he just wanted them to rescue John White and bring him to his granddaughter which in original time, he was not supposed to. Then JB makes an appearance doing the same thing that Brendan and Antonio did to Jonah, landing on Second/Sam and says that Second/Sam is a traitor for jeopardizing the kids, John White and Dare's life. He fires Second/Sam and explains to Jonah that when Brendan and Antonio landed on him in the canoe, it was called a Time Smack and makes the person fall asleep. Second/Sam then gives Andrea his Elucidator and presses a button, but then he falls asleep. A pre-recorded video begins playing. Second/Sam says that he has released the ripple to go on forward. JB screams and gives the kids his Elucidator and sends them into Time Travel. Second's voice comes up on his Elucidator that Andrea is holding and says that they have to hold on to Andrea and press the glowing button to return to 1600. All the kids agree to go back to 1600 but Andrea says that Jonah can't come because she says she wants to protect him. Andrea, Brendan and Antonio make their way back to 1600 while Jonah and Katherine are floating through time travel with JB's Elucidator. Second's voice comes up on the Elucidator and says that he and Katherine will have to beat the ripple to 1611. Jonah and Katherine start doing flips from a force that pushes them which is actually the ripple passing them. Second says that if the ripple passed them an even number of times, they will beat the ripple, and if they flipped an odd number, they are starting behind. It seemed then they beat the ripple, but JB's voice comes on the Elucidator and says that Jonah and Katherine must save 1611 if they want to save JB, Andrea, Brendan and Antonio and Dare from 1600 and return to the twenty-first century. Jonah and Katherine take the chance and land in 1611. When they are traveling through time Jonah finds a piece of paper with John White, Andrea, and Brendan that was drawn by Antonio. Katherine and Jonah get ready to try to save .