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The special chronicles the Straw Hat Crew's first ship Going Merry recreated with brand-new animation. The plot covers an abridged version of the Water 7 and Enies Lobby arcs, from Luffy and Usopp's fight and Robin's disappearance to the crew's battle against CP9 to get Robin back, and the crew's final farewell to the ship.
During a lull in their travel, the Straw Hats are milling around the Thousand Sunny. Usopp, Chopper, and Brook head out to explore the surrounding ocean in the Mini Merry II. Brook asks about the Merry, since he joined after the crew had acquired the Sunny, and Usopp and Chopper tell him about their old ship, from her journey from Syrup Village to the events leading up to her end during the Water 7 and Enies Lobby arcs.
The full invasion of Enies Lobby is not shown; it starts around Luffy's battle with Blueno.
As per the case of an abridged version of an arc, the fights are much quicker; mostly showing the latter part of the crew's battles as the Straw Hats perform the finishing blows on their opponents. Only the battle with Lucci is shown in detail.
The Galley-La and Franky Family involvement in the story is glossed over.
Oddly, despite including scenes of filler material in the story, when Aokiji tells the crew about the dangers of having Robin with them, the scene is on Long Ring Long Land, as opposed to a regular island in the original anime.
The special is apparently meant to take place before One Piece Film Z (specifically Glorious Island), as the crew are in their outfits from the start of that movie. Considering Nami is still wearing her dress from the Z's Ambition Arc, it likewise is set some time after that arc.
According to an interview, the special was completed just mere days before it was set to air. However due to being rushed, there were a lot of inconsistencies with the animation. When the special was released on Home Video, some of the inconsistencies were fixed along with some touch ups of certain scenes.
In Merry's Viking funeral, the song Horizon Knot was used instead of Dear Friends.
The Bridge of Hesitation is missing the tower of the spiral staircase in the exterior shots.