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Word of God acknowledges that Forever was written before several deck archetypes in the real-world Trading Card Game were released. Eternal was written for the purpose of including these deck strategies, but was discontinued due to the author's real-world Heel-Faith Turn clashing with the idea of dabbling in magic.
Additionally, the writer has recently acknowledged that were he to do a remake of Forever, he would input several factors into it that were going to be and had already been placed in Eternal before the latter's cancellation. Among other things, various characters (such as Zander Zabel) would have gotten updated decks with newly-released cards that came out at the time Eternal was being written; as examples of rehashed deck strategies, Abel Drake, Samantha Redman, Laurel Strong and Angel Snow would have received (respectively) Lightsworn, Volcanic, Venom and Ice-themed deck archetypes; Jaden Yuki would have been a member of the Duel Monsters World Tournament Committee; Gabriel Roman would have been included as a major character; the JUDAS members would have wielded the Shadow Charm Items and the Earthbound Immortals instead of the Millennium Items; and potentially more characters with more deck archetypes would have been included throughout the story, culminating in more entrants in the Dueltropolis tournament than the 32 that the fanfic wound up portraying in said tournament.
According to the author, an alternate scenario for the JUDAS arc would have had Kyo being the one to go to Egypt instead of Yugo, Odachi having a grudge on Ryou Bakura instead of Yugi Muto, and Ryou and Rebecca having been married. Under the same scenario, Yugi and Téa would have been married, making Téa Yugo’s mother by proxy.
Listed below are several plot points that would have made it into Eternal had it continued:
During the story, Janus has a nightmare about Racquel being caught in a car bombing, followed by Drake Phoenix blaming him for it. Drake's grudge against Janus would have been revealed to be because of this incident taking place when they were children, with Drake blaming Janus for not being able to save Racquel in time. Except, said Love Interest would have turned out to be Not Quite Dead, but in fact moonlighting in the present day as the Jewel Duelist.
Chazz Princeton would have had a supporting role, with both of his older brothers showing up in villainous roles.
The case of the students who went missing at the Abandoned Dorm (a plot point in GX that was never fully resolved) would have played a pivotal role in the plot, in that their still-living relatives would have come forward to call out the entire Duel Academy for not completing the investigations into that mystery.