On the way to Icirrus City and Ash’s next Gym battle, our heroes lose their way among the many twisting tunnels of Twist Mountain. They get some help from a Pokémon archeologist named Ferris, who has just discovered a Cover Fossil, a fossil of the ancient Pokémon Tirtouga! He’s trying to tell them about it when his boss, Sierra, points out that they’re in a restricted area and asks them to leave.

Ferris invites the group back to his house, where he tells them an unusual story: when he was a child, he actually met and played with a Tirtouga inside the mountain! He has a theory that time behaves strangely in certain parts of Twist Mountain…

Meanwhile, Team Rocket’s Dr. Zager is directing Jessie, James, and Meowth to steal the Cover Fossil so he can restore it to life! He explains that they need Tirtouga’s energy to travel back in time using the same time warp Ferris had experienced as a boy. Their devious plan is to go back to the past, steal as many ancient Pokémon as possible, and bring them back to the modern world, thus enabling them to take over the Unova region. Our heroes will have none of it, however, and the battling begins.

Team Rocket has built many defenses into their equipment, and our heroes cannot seem to penetrate them. In the commotion, the restored Tirtouga escapes, with Ash and Ferris frantically giving chase. They must try to convince the angry Tirtouga they mean no harm, while the members of Team Rocket are determined to catch it for themselves! Who will prevail?