Season 1 of Thunderstone premiered on February 12, 1999.

Season one revolves around Noah's adventures in Haven. As he brings more and more animals from the past to inhabit Haven and continues to jump back and forth through North Col, Haven, and the past before the Nemesis Comet hit, he attracts attention from the Triumvirate in North Col and the Shadow Master in Haven.

Season 2 of Thunderstone premiered on August 13, 1999.

With the Shadow Master and his minions defeated, Noah stays at North Col but misses Haven and is tempted to go back. When he does, he becomes stranded since there is no longer any thunderstone left, or so it seems. In this season, the plot revolves around acquiring a large Thunderstone Cube, which Noah learns about from fugitives from the future, named Mayah and her brothers, who brought it there under a lake.

Season 3 of Thunderstone premiered on June 16, 2000.

Noah is recognised for his genius, and this season begins with experimental wormholes of his design. This allows him to set up a space colony. The people from the future of this space colony wish to assassinate young Noah, because his future self was said to have murdered their parents. They use Noah's time travel technology and make several attempts on his life. The season involves Noah trying to find the truth about what happened and making peace with these people.