The story consists of the following sagas and story arcs:
Saga 1: East Blue Saga (chapters 1-4)
New Romance Dawn Arc (chapters 1-2) (begins after the manga's Arlong Park Arc note It was mentioned that Cross had been on Soundbite's island for two weeks before the Straw Hats found him, and that was a week after Arlong's defeat, so it's likely that Cross arrived in One Piece just when Luffy was setting sail)
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Loguetown Arc (chapters 3-4)
Saga 2: Alabasta Saga (chapters 5-25)
Reverse Mountain Arc (chapters 5-6)
Whiskey Peak Arc (chapters 7-9)
Little Garden Arc (chapters 10-12)
Drum Island Arc (chapters 13-14)
This Bites! The Inevitable Holiday Special! (posted between chapters 15 and 16; set between Drum Island and Alabasta)
Alabasta Arc (chapters 15-23)
Ocean Trips (chapter 24)
Octopus Shogunate (chapter 25)
This Bites! The 1000th Review Spectacular (posted between chapters 30 and 32; set between Alabasta and Jaya)
Saga 3: Sky Island Saga (chapters 26-33)
Jaya Arc (chapters 26-27)
Skypiea Arc (chapters 28-31)
G-8 Arc (chapters 32-33)
Saga 4: Water 7 Saga (chapters 34-44)
Long Ring Long Land Arc (chapters 34-35)
Omatsuri Island Arc (between chapters 35 and 36)
Water 7 Arc (chapters 36-38)
Enies Lobby Arc (chapters 39-42)
The Awe-Inspiring Kancolle Affair! (posted between chapters 42 and 43; set ?)
Post-Enies Lobby Arc (chapters 43-44)
Saga 5: Thriller Bark Saga (chapters 45-52)
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Ice Hunter Arc (chapters 45-46)
Thriller Bark Arc (chapters 47-52)
TheRealEvanSG OMAKES - CANON: Tales of the World (posted between chapters 49 and 50; set during the Thriller Bark Saga)
Crossing the Rainbow Mist (posted between chapter 50 and the forthcoming chapter 51; set between Ice Hunter and Thriller Bark)