The first Chrononauts series opens in Southeast Turkey, where Dr. Corbin Quinn is led to an ancient megalith housing an F-14 Tomcat fighter plane. Back in Texas, Corbin recounts the experience to his friend Dr. Danny Reilly. Corbin theorizes that the plane is one-in-the-same with a fighter plane that went missing in the 1970s. According to Quinn, the plane is just one of several time-displaced artifacts that has recently been discovered. Quinn invites Reilly to join his research team at the government-sponsored Chrono Division.
Several months later, Quinn and Reilly launch the satellite Mark Twain-One into the time stream, allowing television viewers to see the Battle of Gettysburg for the first time. Several months after that, Quinn and Reilly debut their time-travelling Chrono Suits, designed by Reilly himself. The suits allow the two to travel through time and run on batteries that last one hundred years time.
Before time launch, Corbin ruminates over the loss of his alcoholic father, whom he never made time for. He then calls his ex-wife Rachel and apologizes for never making time for her either. Danny kisses goodbye to his girlfriend Cindy and promises to be careful. Quinn enters the time stream first, but he is quickly knocked off course. He crash lands in Samarkand in 1504. Reilly follows Quinn into the time stream to rescue his friend.
Reilly emerges from the time stream in the middle of a battle between a Moghul army and a Samarkandian one. The Samarkandians, led by their general Sarvar, wield time-displaced weapons and drive time-displaced vehicles, giving them the edge over the Moghuls. After the battle, Reilly reveals his identity to the belligerent Sarvar. Recognizing Reilly’s name, Sarvar brings him to the capital of Samarkand.
Reilly learns that Quinn has become king of Samarkand and often upgrades his army with time-displaced equipment. While Reilly believes the two have been separated for forty minutes, Quinn reveals that he has been missing for four years. Quinn was able to return home at anytime but preferred not to because his life had fallen apart. Quinn shows Reilly that he’s been having fun across the time stream, even dating multiple famous women at once. Quinn invites Reilly to join him in adventuring through time, and Reilly accepts after disconnecting the tracking device in his Chrono-Suit. After witnessing the truth of the situation, Chrono Division sends a team of black ops agents led by Mannix to kill Quinn and Reilly before they completely destroy time. The team tracks the Chrononauts by tracing their batteries.
In 1920s New York, Gay Orlova, one of Quinn’s lovers and the girlfriend of mobster Lucky Luciano, discovers that Quinn has been cheating on her with other women. Gay decides to reveal the truth of her tryst to Lucky to get revenge on Quinn, even though she knows she will suffer just as much as he will.
Quinn and Reilly engage in numerous thrills across the time stream, including flying jets through the prehistoric era, meeting baby Jesus, and fighting in medieval wars, among other activities. They even take credit for numerous pop culture properties like Beatles songs, the Harry Potter series, and Breaking Bad. While touring with the band Morrissey, Reilly receives a telegram from himself stating that Quinn has been killed and that he himself has been fatally wounded. The telegram tells Reilly to show up in 1929 with a fast car to undo the predicament.
Lucky Luciano and his men ambush Quinn while he is in the shower. They burn his Chrono Suit, stranding him in the past. As Lucky is about to execute Quinn, Mannix’s Chrono Division team kills the mobsters. They let Quinn live until they can find Reilly. Quinn escapes from Mannix’s team and is rescued by Reilly in a 1970s De Tomaso Pantera.
Reilly and Quinn are pursued in a car chase through the time stream, passing through 1960s Miami, 1890s London, 200s Rome, 1940s Kursk, 1960s Dallas, and 200s B.C. China. In the 1450s Grand Canyon, one of Mannix’s soldiers falls to his death. Mannix and his team are stranded in a prehistoric period when a T-Rex smashes their vehicle. Mannix reveals that he survived the T-Rex attack, but is promptly stomped on. Arriving in 1504 Samarkand, the two decide to abandon Danny’s Chrono Suit to prevent Chrono Division from tracking them any further. They plan on starting a new life in 1504 London, but are captured by Sarvar, who now wears Reilly’s suit.
Sarvar’s men throw Quinn off a cliff and leave him to die in the desert, while they torture Reilly. Quinn embarks on a long journey around the world to the Grand Canyon, where he finds the corpse of one of Mannix’s men. Quinn uses the corpse’s Chrono Suit to amass an international, inter-time period army. Quinn leads his army in an assault on Samarkand, killing Sarvar with a jump jet.
Reilly convinces Quinn to fix the time stream after telling Quinn that he can still use the suit to be there for his loved ones whenever they needed him. Quinn’s personal life is repaired. When Quinn and Reilly complete their adventure, they discover that their activities still slightly altered the time stream, causing Reilly’s girlfriend Cindy to marry Mannix. The series ends in Reilly’s frustration.