Thirteen-year-old Jonah, his 12-year-old sister, Katherine, and their friends Chip and Alex, have been transported through time by a mysterious man named JB. It seems that Jonah, Chip, Alex and other children from their town are actually misplaced figures from history. JB and other time purists realize the problem with having these children missing from the past and hope to return the children to their proper places in time.
In book one, JB and others kidnapped Jonah, Katherine, Chip and Alex, and hold the children in a cave. When given the opportunity, Jonah steals several of JB's tools, and he and Katherine go with Chip and Alex as JB initiates the time-traveling process. Through the Elucidator, one of JB's machines, Jonah can hear the time purist telling him and Katherine to come back.
Chip and Alex are meant to return to the 15th century, but Jonah and his sister aren't. Jonah threatens to mess up history even worse if JB doesn't let him try and right whatever went wrong and then bring Chip and Alex back to the modern world.
The four children find themselves dropped into the bedroom of two young boys. Through the Elucidator, JB explains that Chip is really King Edward V of England; Alex is his younger brother, Prince Richard. The two boys are locked in the Tower of London. Jonah and the others can see the boys' "tracers." Tracers are the ghostly apparitions of Edward V and Prince Richard that are living in the past. Chip tries to Taser his alter self, but the weapon doesn't work on the boy. JB transports the Taser away, warning the children that modern technology is forbidden in the past. Jonah wonders why JB doesn't just transport Katherine and him back. JB has decided to let them try to right history and help their friends return, once the past is set right.
Chip and Alex realize they can join their tracer bodies. When they do, they are able to read the boys' thoughts. The longer they stay inside the tracers' bodies, the less Jonah and Katherine can see their friends. They struggle to physically pull Chip and Alex out of the past. When they do, Chip explains that he seemed to have King Edward's brain, and Edward fears that his uncle, Richard of Gloucester, plans to kill him. JB refuses to tell the children anything about King Edward and Prince Richard's fate, as he doesn't want the children influencing the past. Chip and Alex both feel as if they belong in the past and are ready to accept whatever fate awaits them, but Katherine and Jonah refuse to let them give up the chance of returning to the future.
Although King Edward believes their uncle Gloucester is going to kill them, Prince Richard believes their mother has a plan to save them. The four friends scurry to hide as someone opens the door to the room. They realize the men entering the room can't see them or the tracers, so they will think the princes are missing. Jonah and Katherine remain in hiding, but Alex and Chip return to their tracers so the men will see them. They pick up the boys and carry them to the window. Jonah and Katherine manage to grab onto their friends as the men throw the tracers below. As the men can't see the glow from the tracers, they assume the boys have fallen to the ground. They leave to find the bodies.
Jonah wonders why JB won't bring Chip and Alex back since their historical counterparts are dead. Chip believes it's because JB really wanted Alex and him to die. JB tries to explain what he is doing, but Chip, in his anger, kicks the Elucidator, causing it to malfunction. The children press a restoration button, and the Elucidator ceases to work. The only function allowed is invisibility. Jonah presses that button, hoping for some kind of cover as more guards enter the room to search for Edward and Richard. Luckily, the machine makes them invisible to those in the past, even though the children can see faint outlines of each other. The children must still evade the guards, who will be able to find them if they touch them. One guard gets so close to Katherine that a spark from his torch lights her hair on fire. Jonah puts out the flames, but the guard is convinced that some kind of evil spirit inhabits the room. He and his fellow soldier flee. The children try to figure out how to be more proactive.
In the morning, a maid brings breakfast for Edward and Richard. Unable to see them, she assumes they're using the bathroom and leaves the tray in the room. Jonah and the others sample the food but are unable to eat anything besides the bread because of the spices used. They hollow out the loaf of bread to disguise that it's been eaten. Chip finds that he still retains King Edward's memories. He fills the others in on events since his father, King Edward IV, died. Fighting between the nobles has broken out, as many of the king's relatives from the house of York didn't like the queen's family, who were from the house of Lancaster. His son Edward V had been living with his mother's brother, Lord Rivers. The two had set off for Edward's coronation with a contingent of soldiers. Lord Rivers left Edward at an inn with the soldiers while he went back to meet with the Duke of Gloucester, the brother of King Edward IV. Gloucester had Lord Rivers arrested and then convinced King Edward V to accompany him to London. At first Edward was allowed to prepare for his coronation, but later he became more of a prisoner in the castle. Edward is convinced that Gloucester is trying to take the throne from him.
When they can't get the Elucidator to work again, the children decide to venture out from the palace. Still invisible, they follow a group of nobles aboard a river barge and soon learn they are heading toward Westminster Abbey for the king's coronation. At the Abbey, the crowd cheers for King Richard. Furious, Chip runs after his uncle. Jonah manages to stop him. The children come up with a plan to "haunt" King Richard. As the king prays in a shrine before the coronation ceremony, Chip whispers in his ear that he is a traitor. The king orders everyone out of the shrine so he can talk openly with the "spirit." Chip accuses him of killing the young princes. King Richard asks what he should do, and Chip demands he renounce the throne. The king insists all he's done is for the good of England. As they continue to fight, Chip and the others become visible. Katherine claims their strange clothes are what people wear in heaven. She tells King Richard he'll never know what heaven is like because of what he's done. Chip threatens to haunt Richard for a long time. When the king seems about to let his advisers back into the room, the children flee. While trying to escape the Abbey, they run into a group of monks. They explain that they are foreigners to England, here to see the coronation of the king. They question the monks as to why Gloucester is being crowned instead of Edward. The monks explain that the legitimacy of King Edward IV's marriage to the boy's mother has been questioned. It seems King Edward IV had been betrothed to another woman first. This makes his marriage illegal and any children of that marriage illegitimate. Later, Jonah questions why Gloucester would bother to kill Edward if he'd already convinced everyone the princes were not legitimate. Chip explains that as long as Princes Edward and Richard were alive, Gloucester's enemies could use them to plot treason.
The children believe if they convince the queen, Edward IV's widow, that her sons are dead, they'll be able to go back to the 21st century. They make themselves invisible again and sneak into her room. At first, they see the queen and her daughters weeping on the bed, but then the children are shocked to see the tracers of the princes and their family laughing, in another corner of the room. Jonah and the others realize the princes must have originally survived the fall. Now they must come up with a new plan to get Chip and Alex back to the future. Chip and Alex rejoin their tracers when their family is distracted, so it won't seem as if they've appeared out of thin air. The queen is overjoyed at their return, explaining she thought something had gone wrong with her plan when her advisers couldn't find the boys after their escape. She also breaks the news that King Richard had Lord Rivers and his friends beheaded. There is no one to help the boys reclaim the throne.
Jonah and Katherine wonder what to do next. They also realize that JB knew Chip and Alex wouldn't be killed when they were thrown from the window. They'd never given the time purist a chance to explain his behavior. Jonah turns on the Elucidator. JB tells them he must pull Katherine and Jonah "out of time" so he can explain what needs to be done to save Chip and Alex. Jonah wants to check this option with Chip first, but is unable to disconnect his friend from the tracer. JB pulls Jonah and Katherine from the past into a kind of viewing room. From here, they can watch what is happening in the past, but can't communicate with their friends.
JB tells the children that in the "original" past, the boys went missing. No one knew what had happened to them. Some believed they'd died, some that they hid, and others thought they'd sprouted wings and flown away. Jonah and Katherine had actually helped the situation when they pulled Chip and Alex out of their tracers before being thrown from the window because that would have totally changed the future. Now there is still hope to right things. Before JB can explain things further, he sees King Richard approaching the queen's rooms. Jonah tries to return to the past by running at the "window" they are viewing, but he is repelled. He watches as Richard and the queen talk. Richard tries to convince her that the princes are dead, and she, without revealing she knows they're alive, still manages to threaten Richard's position as king.
JB convinces Jonah and Katherine that Chip and Alex must remain in the past for two more years. Jonah and his sister are angry, thinking that they'll have to wait two years to return home, but JB speeds up the past. They watch as Chip and Alex are sent into hiding. King Richard is shown having an uneasy reign. His best friend betrays him and tries to steal the throne. Richard has him executed. In a moment of happiness, Richard has his son crowned Prince of Wales. A few short months later, the boy dies. Richard's wife dies shortly after, breaking his heart. He believes their deaths are punishment for his sins. Chip and Alex are shown training to fight with swords and growing older. JB has a plan to save them. Jonah and Katherine will return to a pivotal battle between King Richard and Henry Tudor, a rival from France. Although people from the past can't see them, if they are killed in the fight, their bodies will reappear. JB gives them armor to wear in case that happens.
Moments after they are transported back in time, they run into King Richard. They are invisible, but he knows they're with him. He believes they are the spirits that spoke to him in Westminster Abbey. He tries to explain that he had the princes killed because he truly believed that putting such a young king on the throne would ruin England. Their mother's family would have destroyed the monarchy. He begs for forgiveness. Katherine accidently offers him hope that he might one day see his beloved wife and child again in heaven. When he begs to know how, Jonah tells him that if he's sincere, his sins will be forgiven. Katherine tells him he must figure out the way himself. Richard promises to pray about what he must do.
Katherine and Jonah try to find Chip and Alex. Katherine calls Chip's name out to a formation of soldiers. One of them turns his head toward the sound before turning back to watch the battle, but when Katherine and Chip approach him, they discover it isn't Chip. Chip is nearby however, but doesn't respond to Jonah's pleas to separate from his tracer. Since Chip and Alex must choose to leave the past, Jonah fears that his friend is lost forever. Katherine tells Chip that she has turned down dates with many boys because she is in love with him. That jars Chip out of his tracer. Then he pulls Alex from his tracer so that they can hear JB's plan. Before Jonah can explain, King Richard appears. Chip and Alex rejoin their tracers so they can fight. JB has told Jonah that King Richard needs to see the princes before Chip and Alex can be pulled back to future.
King Richard sees his nephews. He dismounts his horse and kneels before Chip. He admits his sins but pledges to return the crown to the prince if Henry Tudor is defeated. He rejoins the battle, even though his side is losing, vowing that he fights to defend Prince Edward's crown. When Edward, who is Chip, sees Richard killed, he runs into the conflict to reclaim the crown for himself. Katherine follows to try and stop him. Even though Jonah tries to convince him that he will die on the battlefield, Chip thinks it is honorable to die fighting for something. Jonah argues that Chip is acting just like his adoptive father, a selfish man.
After all, Katherine has just confessed she loves him. Would it be fair to cause her so much pain when he could prevent it? As the battle continues around him, Chip separates from his tracer, leaving his opponent to think the prince has disappeared. Another soldier protects Chip from several blows as he asks Katherine if she'd really miss him. She admits she'd rather save his life than grieve for him. Chip manages to save Alex from being cleaved by a battle-ax. JB brings the children back to the 21st century.
The children are returned to the cave where the other kidnapped children are being kept. The soldier, who protected Chip and Alex, returns as well. He is actually another time purist assigned to help the children in the past, without their knowledge. JB praises their work. Jonah and the other kids ask JB to let them go back to their homes to readjust to the new reality. He doesn't have to worry about them telling anyone; after all, who would believe their story? JB agrees, and the kids go home, knowing that sometime soon they will be asked to return to the past.
A week later, JB arrives to talk with Jonah, Katherine, Chip and Alex. He explains that history has been corrected. Alex wonders if the fact that they're still alive — since he and Chip were supposed to die — will change the future. JB explains that the present is in a state of flux anyway because of the original tampering in the past. Alex and Chip should live their lives as normally as possible from here on. JB then tells the children the real reason for his visit. Jonah and Katherine did such a great job fixing the past and rescuing Chip and Alex, he wants to give them the chance to help another girl. It only takes them a moment to agree, as they don't want anyone to have to go through the experience alone.