Osamu incorrectly refers to Clown Zombie as Crass Clown.
During Jaden's flashback to his childhood, his friend duels him and attacks directly with Skull Servant, Dragon Zombie, and Clown Zombie but when their card form is shown, Clown Zombie showed the box for ATK and DEF in addition to the box for the card's text when it should've looked like Dragon Zombie and Skull Servant.
Aster: (about Yubel) What do I care about some AWOl duel spirit?
Zane: You tell me. Ah... clutches his chest in pain
Aster: You okay? What's wrong?
Zane: (quickly composing himself) Nothing. I'm fine.
Jaden: It's me. It's my fault. Everything was because of me. It's all my fault.
Zane's condition, first seen briefly here, will be revealed in "The State of Syrus".
The Subtitle is changed from "Quest for the Rainbow Dragon" to "Into The Shadows".
The Bio-Bands disappear after the students return from the alternate dimension.
The theme song changes a little bit to feature a few new images, and Professor Viper is replaced with Yubel.
Everyone now knows that Jaden can see duel monster spirits and learn that their new enemy is Yubel, one of Jaden's old monster spirits. No one believed this at first when Aster explained to them that Jesse was the only one who could control the Crystal Beast Cards. But with the knowledge they now have, they now believe that Duel Monster Spirits exist.