In a world where dragons and men coexist, Weyrleader F'lar and his Weyrwoman, Lessa, push past personal differences and work together to save Pern from deadly spores known as Threads that fall to the ground with the Red Star's orbital passing. In the past, six Weyrs filled with weyrfolk, dragons and their riders fought this alien invasion using dragon flames to sear the Threads before they reached the ground. Yet, as the threat draws near, five of six Weyrs sit empty, leaving F'lar, Lessa, and a handful of dragons and dragonmen of Benden Weyr to save all of Pern. The two turn to the ancient Ballads, Traditions and Records for help. When Lessa accidentally visits the past while learning to fly her dragon queen, they believe the answer to the Question Song is to fly dragons between times to the past in order to seed the dragon population and give them time to grow before the next battle.

As the story opens, Lessa hides behind the disguise of a filthy kitchen drudge within Ruath Hold where she awakens with a sense of danger. Her special ability touches the watch-wher's mind, but it does not sense the danger. The threat is unfamiliar. Danger emanates from the east and the west. Her eyes drift to the Red Star dominating the sky at dawn—a recent occurrence. The worst of the danger will come from the east.

F'lar senses Lessa's power and sees through her disguise while she is unconscious. After talking to her, he carries her to Benden Weyr in hopes she is one to Impress with the queen. When the queen dragon hatches, Lessa is chosen by the hatchling. This thrusts the girl into the position of Weyrwoman overnight. She uses her secret abilities discreetly, but her hidden skill of communicating with all dragons creates a bond between her and the beasts. This bond of trust paves the way for the future when dragons and riders are forced to fly between times in an effort to repopulate the diminished dragon population.

With the discovery of Threads falling over Nerat, flying between times becomes a reality for the dragons of Benden Weyr and their riders as they go back two hours to fight Threads at dawn. The battle is successful but takes its toll. The few dragons and trained riders will not be enough to fight the Threads day after day for years. This reality gives birth to a plan to send a queen and a handful of others ten years into the past to grow the dragon population and bring their riders to maturity. This venture is not enough to keep up with the steady stress of fighting the Threads. However, it gives birth to Lessa's idea as she reads the Question Song. Along with references found on a long lost tapestry, she decides to risk traveling back four hundred years to a time before the Weyrfolk of the other five Weyrs disappeared. If she arrives safely, she plans to ask their help to fly forward in time to fight the Threads along with F'lar and the handful of others.