- Unlike the original ending of Season 5, there are two endings to the game: the normal ending, and the True Ending. Upon accomplishing the true ending by collecting all 50 of the Corrupted Emperor's Kamon and defeating Aku, Jack is seen under the cherry tree in the original finale. However, after the ladybug flies off, the camera pans to reveal that Ashi had survived and managed to live after her marriage to Jack. As such, Jack finally gets his happy ending. And it's canon!
- The fact that this came after fans had basically petitioned for this following the original ending's airing and the overall joyful reaction to it. To repeat, fans cared so dang much for Jack (and Ashi!) that they fought to get a true, 100% happy ending, and that's exactly what happened!
- Besides Ashi surviving, there's a subtle difference between the show's ending and this game's True Ending: In the final scene of the show's Grand Finale, light shines on everything but Jack, representing the show ending on a bittersweet note. Here, light shines on not just the grove but Jack and Ashi as well, symbolizing the happy ending for the two. Furthermore, the scene started to light up when Ashi is revealed to still exist.
- In the city level there's a nod to Aku's late voice actor Mako. There are posters plastered on the walls, and one is of Aku in an advertisement for an acting course, that is presented by the "Mako Center for Extremely Awesome Acting". Forever shall Mako be remembered his acting capabilities that gave voice to the Master of Darkness, and for helping inspire the next generation of actors.
- The challenge of finding and speaking to all of the Scotsman's Daughters is titled "Uncle Jack", suggesting that even though Jack turned down the Scotsman's offer to marry one of them, they still consider Jack an Honorary Uncle.
- Even though he's basically trapped, thankfully Jack finds his old allies in there with him. Scotsman, Scotsman's Daughters, Sir Rothchild and Da Samurai; all of them lend a hand to Jack in defeating Aku once and for all.
Heartwarming / Samurai Jack: Battle Through Time