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It follows the adventures of Liam O'Connor, Saleena Vikram, and Madelaine Carter, three teenagers pre-destined from the dawn of time to meet early, untimely deaths. Liam O'Connor should have died on the Titanic in 1912, Madelaine Carter was supposed to die on a doomed plane above America in 2010, when a mysterious old man offers both the chance to escape, but at a cost: they would not be able to return to their lives ever again. Saleena Vikram's supposed "death" was not spoken of in the first book.
They all awaken in the Arch under the Williamsburg Bridge in New York in a 48-hour time bubble, running from September 10th, and September 11th. The time bubble resets back to September 10th at the end of the 11th, meaning the TimeRiders will relive those two days, over and over, as long as they remain within the time bubble.
The reasons, as Foster explains, is that using the time of the collapse of the twin towers, the agents can go unnoticed.
Moments before their deaths, an old man known as Foster recruits Liam O'Connor, Madelaine Carter, and Saleena Vikram. They awake in 2001, New York. Foster introduces them to the field office. Right after the three agents awake, a seeker appears, and they are forced to leave.
Once outside, Foster explains that when people travel through time, they move through another dimension for a brief time, and it is possible to bring back a seeker by accident. The last team was killed by seekers, therefore needing a replacement.
The four explore New York. Later, the group explores the Museum of Natural History. Connor and Carter sign the Guestbook and learn that older versions of the Guestbook are stored in the basement of the Museum.
After explaining the 48-hour time bubble, Foster assigns roles to the three members: Liam O'Connor as the field agent, Madelaine (referred to Maddy in the books) Carter as the team leader and Saleena(referred to Sal in the books Vikram as the observer. As the field agent, Liam is the one that travels through time with their fourth team member, a support unit named Bob (for this book). Maddy is the one that works with the computers and makes decisions once Foster leaves), and Sal as the observer is the one that notices shifts in the timeline.
For their training mission, Foster brings Connor and Bob to Dallas, Texas on the 22nd of November, 1963, the day that Lee Harvey Oswald assassinated John F. Kennedy. They alter the timeline by distracting the killer, causing John F. Kennedy to live instead of die.
In the present, Vikram detects a change. In the office, Carter also detects it. Reading an article about an upcoming Mars mission, she is surprised that JFK is still alive and is the one behind the program. She deducts that Connor, Bob, and Foster must have traveled back to stop the assassination of JFK.
In the past, Foster explains to Connor that the assassination of JFK is an example of a historical event where history corrects itself. They watch as hidden assassins shoot and kill JFK. They return to the present.
Foster is delighted that Carter had figured out exactly when and where they had traveled.
Not long after their first training mission, the timeline is altered when Dr. Paul Krammer, along with a group of men lead by Karl Hass, a former soldier, travels from the year 2066 back in time to 15th April 1941, using the first time machine made by Roald Waldstein.
One of the first horrors that Krammer realizes is when two of his men fuse together.
Engaging in a battle with Hitler's troops at the eagle nest, the eventually meet Hitler face to face. Striking a deal with Hitler, Hitler calls off his men outside, and Krammer helps Germany to win World War 2 using advanced technology and knowledge from the future. Once the War is over, Krammer kicks Hitler out of power and takes over himself.
In the present, Sal Vikram detects the shift and hurries back to the office. Connor and Bob are sent to the exact date of when German Forces forced the American Government to surrender. After gathering information, they attempt to return. With tensions high between the Germans and the American prisoners, the two miss the two-time windows. One of the German soldiers resting near the window was instead transported into the office. When he returns, he fuses with another soldier.
When Connor gets transported to a prison camp, Bob initially decides to return with the information in the 3rd time window but considers Connor as a friend and decides to save him.
In the present, another shift happens, resulting in New York becoming a wasteland, filled with mutated creatures that feed off of each other. Vikram is still in times square when it happens, and comes in close contact with the mutants. Carter and Foster get to her in time, preventing casualties. Later, Vikram learns that they are cannibals. The three speculate about the cause of the second shift.
Back at the office, they find that their engine has shut down, and they need Diesel to keep the time machine running and eventually bring Connor and Bob back from the past. Vikram is terrified but agrees to go with Foster and Carter to find Diesel.
In the past, Bob starts raiding prison camps in attempt to find Connor, and soon, prisoners begin to join him, attacking camps and freeing prisoners, indirectly starting a resistance movement. After 6 months in his camp, Bob finally reaches Connor and frees him.
Onboard the ship where Krammer and Hass, one of his men work, Krammer is shown the fused body. Realizing this is the result of time travel, Krammer starts to lose his mind. Eventually to the point where he believes that the devil is after him. Building a device that would largen the effects of the atomic bomb that is armed, he gets ready to end humanity once and for all. When Karl objects and tries to stop Krammer, Krammer has him executed. A week later, he activates the bomb (This happens after Connor and Bob leave the past).
In the present, the team finds Diesel in an abandoned subway. They encounter mutants, and Foster kills them with his shotgun. Bringing the oil in small containers, they return to the office and power the engine. Using the now functioning engine, they send Tachyon particles to the past to transmit a message.
In the past, Bob receives the message, and he and Connor leave the rebel camp to make it to the coordinates that the office has given them for a time window. On the way, Bob informs Connor that the agency can only bring one back to the present and that he will soon self-destruct. When the time window fails, Connor remembers the guest book of the museum and has an idea to leave a message for Carter, Vikram, and Foster.
Meanwhile, in the present, Carter also remembers the guest book. The three leave the office and travel to the now deserted museum, and down into the basement.
In the past, Bob and Connor arrive in New York, with stolen German uniforms and travel to the Museum of Natural History, where everything is to be burned. Apparently, Krammer believed that the only way to have a fresh start is to forget all history and mark now day one.
Connor and Bob trick their way inside, where they meet the same guard they saw in 2001 monitoring the guestbooks. Leaving a message with the coordinates that they believe would be fitting for the time window to bring them home and their date, they hide the book and leave clues on where to find it.
In the present, the team uncovers all of the clues and almost gives up until Vikram finds the book hidden behind a block of loosened concrete. Ripping out the page of where Connor has written on, they attempt to return to the office. When mutants start to gather, they decide to cut through Central Park. It soon appears to be a trap that the mutants have set up. Vikram is taken, and Carter attempts desperately to rescue her. Foster manages to persuade Carter, telling her that Vikram might return if they change back history.
Back at the office, they examine the coordinates, and Foster finds out that the coordinates that Connor and Bob have selected match up with the office's, therefore saving them plenty of energy. While waiting for the time to open the window, the mutants find their office and break in using the weak spots. Carter and Foster desperately defend themselves using the nine shots left in his shotgun. Foster says to leave two bullets for each of them.
In the past, Bob and Connor empty out the building and await the time window. They discuss Bob's self-destruction during that time. When the time has exceeded and the time window still hasn't appeared, Connor gets ready to live in a world where Nazis are in control. Bob suddenly detects Tachyon Particles, and they step through the window.
They arrive safely, only to find Carter and Foster in danger. Bob defends the agents and fights off the mutants, with a little help from Connor.
Informing Foster of the events, they are sent back to the forest outside the Eagle nest, at the exact time where Krammer and his men appear. Bob defeats most of the men, but due to being injured heavily, collapses in the snow. Connor informs Krammer of the future that he has created and begs him and Karl to stop. The unintentional distraction is enough for Bob to finish off Krammer, Karl and the rest of the Time Travelers.
In the present, Foster and Carter experience two-time shifts, which takes them back into the world that they know.
As sirens sound, Connor and Bob enter the time window and return to the year 2001.
Vikram magically appears, unharmed and with no memory of the mission.
Bob's AI system is transported into a computer, while he is having his body regrown.
Carter and Foster walk in New York. Foster bids them good luck and Farewell, as he will soon die.