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There were many differences between the Japanese and English versions of the second series anime, such as even changing dialogue that had no threat to children to edit. However a few of these changes were almost always there, especially during the episodes that included Duels, which were mainly all of them.
Original Japanese Version
- The two main differences in all the episodes were how the dub episodes were edited and had scenes removed, and the opening theme song in the different versions. The theme song had different artwork and different scenes from each version's season for their respective songs, since some scenes were cut out in the dub's seasons and therefore were unable to be added in the dub's songs, although they occasionally shared certain scenes in some seasons' songs. Although the scenes and artwork in both versions' songs changed with new seasons, the English dub always had a theme song with the same tune and the same words ("It's time to D-D-D-Duel!"), while the Japanese songs changed both their tunes and words.
- Both versions had Shadow Games played, with penalty games following, but only the English dub included the Shadow Realm. Characters did not have their minds or souls banished to the Realm, although the loser's penalty still included damage to their minds or souls. Also, characters would die or be seriously injured instead of being sent to the Realm.
- The titles of the episodes were always different; in the dub, when the episodes were about a fight that continued for more than one, they would have the same name included with "Part 1" and on and on until the battle ended.
- The Japanese version of the tiny rectangle that shows both a character's Life Points and a monster's ATK and DEF is a different color, with phrases not included in the dub. The rectangle is gray, and for Life Points, it has "LP" above the number, while the monster's points, have (in Japanese) words on the left of the respective number that most likely mean "attack" and "defense", with the attack ones on top and the defense on the bottom, although this position of the monster's points is the same in the dub.
English Dub Version
- The seasons were greatly edited in the English dub, such as creating the Shadow Realm, changing conversations, editing out weapons such as guns or knives, and completely cutting out scenes that usually weren't seen for American children to watch, like physical violence. These edits had the possibility of changing the plot and even character development, especially in the Battle City tournament.
- For example, Marik wanted both the Millennium Puzzle (for the Pharaoh's power) and the 3 Egyptian God cards for world domination in the dub, while in the original he wanted both those 4 items in order to become the Pharaoh himself so his family could live above ground and to kill Yami Yugi because of his belief that the Pharaoh had ordered Shadi to kill his father instead of his second personality, Yami Marik, along with his anger again of how his Ishtar family had lived underground, suffering without sunlight and such, for thousands of years to protect the Pharaoh's tomb.
- Also, for character development, in the dub Joey Dueled in the tournament to help Yugi save the world against Marik, but in the Japanese anime, he was trying to become a much better Duelist and earn the "right" as a "True Duelist" to Duel Yami Yugi.
- As stated above, the Shadow Realm was created in the English dub in order to make this version of the anime more "child friendly", so the protagonists were able to rescue characters from the darkness after being banished there because of shadow magic from the Millennium Items, usually due to penalties of Shadow Games, while in the original the characters had died or were in danger of dying. In most episodes of great danger, the Shadow Realm caused a very different change in the plot that would involve being banished to eternal darkness instead of eventual death, especially in the Battle City arc. For example, when Yami Yugi Dueled Arkana, the buzz-saws were normal ones in the original that would cut off the loser's legs with the possibility of killing him because of the amount of blood lost, but in the dub, they were glowing and would send the loser to the Shadow Realm upon contact.
- During episodes that had duels or other battles go on for more than one episode, there was always "To Be Continued..." at the bottom of the dub episode's ending scene, until the final episode that ended the fight, which would not include the phrase. These episodes that had battles that went on for longer than one episode also continued their name, with "parts" in the title, such as "Village of Vengeance - Part 1", and would continue on until the fight ended. However, the Japanese version did not do either of this; every episode had a different name. The English rectangle of Life Points and a monster's attack and defense points is blue with light yellow circular stripes, but there are not any words or letters, like "LP" in the original, although a monster's attack points are shown at the top and the defense points are at the bottom, just like the original.