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Some of the key plot points of the Skypiea Arc have changed:
The Straw Hats being attacked by Wiper and meeting Gan Fall and Pierre are omitted. The crew instead meet the two on Angel Beach.
The Straw Hats' journey from the White Sea to the White-White sea has changed, and the Straw Hats' crime for which they are charged is invasion. Furthermore, instead of Amazon asking for the entrance fee, they are carried there by a Speedy Shrimp.
Conis' introduction has changed to her being chased by Sky Beasts and rescued by Gan Fall and the Straw Hats.
Nami test driving the Waver is shortened, and she does not travel to Upper Yard and witness the priests' judgment.
The Speedy Shrimp takes the Merry to the altar with only Chopper and Su on-board, with Nami following on the Waver, while Zoro, Robin, and Conis travel by another Dial Boat.
Since Conis remained on the Going Merry when Enel attacked, she learns about Enel's plot here, instead of later on due to the removal of her father Pagaya and Enel's former soldier who warned them in the original storyline from the special.
Aisa's role had been severely reduced and she never meets nor befriends Luffy and Nami since she never left the Shandian village on her own. As a result, her ability to use Mantra was never revealed in the special.
The part of Gan Fall, Pierre, Nami, and Aisa also being swallowed by Nola was omitted.
The Angel Island residents attacking Conis is omitted.
Gan Fall is used in place of McKinley to help Conis convince the Angel Island residents to evacuate and he and Pierre stay with them and the Shandians until the battle is over instead of with the Straw Hats.