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Years after the events of Fossil League, a young boy named Kenta decided to follow his father's footsteps to become a Dino Fighter champion. A paleontologist named Dr. Tokudaiji and his assistant Mio persuaded Kenta to work for them and help them with their research using a new time machine. He met an Albertosaurus named Al, which became Kenta's first dinosaur. However, after a battle against a girl named Ran and her Gorgosaurus, Al was mortally wounded. Kenta will do anything to take care of Al while trying to become a Dino Fighter champion and help Dr. Tokudaiji with his paleontological research. Meanwhile, an evil scientist named Professor Fogle is trying to mess up the Dino Fighter championship using illegal means, from manipulating Kenta's friends to stealing valuable fossils.