Kivrin Engle, a young historian, specializing in medieval history, asks her reluctant instructor, Professor James Dunworthy, and the authorities running the project to send her to Oxford in 1320. This period had previously been thought too dangerous because it stretched the time travel net 300 years earlier than it had ever been used before.
Shortly after sending Kivrin to the 14th century, Badri Chaudhuri, the technician who set the time travel coordinates for the trip, collapses. An early victim of a deadly new influenza epidemic disrupts the university and leads to the city being quarantined. Kivrin also falls ill as soon as she arrives in the past. After several days of fever and delirium, she awakens at a nearby manor, whose residents have nursed her. Being moved by her rescuers causes her to lose track of the “drop point,” the location where she arrives and must return at a prearranged time to get home.
The narrative switches between Kivrin in the 14th century and 2054/2055 Oxford during the influenza epidemic. Kivrin discovers many inconsistencies in what she “knows” about the time: the Middle English she learned is different from the local dialect, her maps are useless, her clothing is too fine, and she is far too clean. Kivrin fakes amnesia, afraid the background story she originally concocted would have inconsistencies as she tries to find the drop point. Meanwhile, she becomes semi-integrated into society, bonding with the children Agnes and Rosemund. In the other timeline, Dunworthy tries to determine if Kivrin is safe as Oxford collapses into a panic. He befriends his friend Mary’s grand-nephew, Colin, and they become allies.
In future Oxford, fears grow that the virus causing the epidemic has been transmitted from the past via the time travel net. This causes Balliol College Professor Gilchrist, acting head, to order the net closed, effectively stranding Kivrin in the past.
Kivrin and Dunworthy realize that she arrived in England in 1348 during the Black Death pandemic, more than 20 years later than intended. Because there’s no slippage (the time shift between a traveler’s intended and actual arrival date), it’s believed that Badri, delirious with illness, input the incorrect coordinates. It turns out that Badri contracted the influenza virus from human remains at the archaeological dig when he had been helping there, starting the epidemic at future Oxford.
The Black Death cuts a swathe through the Middle Ages, just as disease overwhelms the medical staff of the 21st century. Of those able to help Dunworthy, many die, including his friend Mary Ahrens, a doctor treating the infected who herself succumbs. Dunworthy himself is stricken by the disease but survives.
Meanwhile, in the 14th century, two weeks after Kivrin’s arrival, a monk infected with the plague comes to the village. Within days, many residents of the town fall ill. Kivrin’s arranged retrieval date passes with neither side able to make it. At last, Dunworthy arranges for Badri to send him back in time to rescue Kivrin.
In the Middle Ages, Kivrin can only watch while all the people she has come to know start to die from the Black Death. Dunworthy and Colin then find her. The three return to 21st century England shortly after New Year’s Day. Colin excited by the concept of time travel, saying he will go to the Crusades when he is old enough.