"Born and bred a warrior, Samurai Jack is thrust into the future by his nemesis aku. In his travels, Jack learns of a time portal that can reunite him with his ancient ancestors. Now he must battle aku's minions across burning villages, massive forests, and the bustling aku City to find the portal!"
— Back of the case
Tropes back, back in this game include:
- 100% Completion: Rescuing all of the villagers and obtaining all the relics makes the game complete.
- Bittersweet Ending: As with other plots from the franchise, Jack failed but did it with the help of friends.
- Bullet Time: Jack can go through Zakai Mode by slowing down time to a crawl.
- The Bus Came Back:
- Exdor from "Jack versus the Ultra-Bots" returns in this game.
- Mad Jack returns in this game.
- Excuse Plot: Jack has another attempt to get back to his timeline but he is failed yet again.
- Exposition Fairy: The voice of the Emperor.
- Leaning on the Fourth Wall: Aku has made brainwashing video games at Aku City, with Jack wondering what video games are.