At Edd War, the Roger Pirates prepare to clash with Shiki and the Golden Lion Pirates. Shiki wants Roger to join him with his knowledge of an ancient weapon, but Roger refuses and eventually escapes the fight when a huge storm wipes out half of Shiki's fleet. Years later, after Roger becomes the Pirate King, Shiki discovers that he has been captured. Hearing this, he heads to Marineford, is defeated by Garp and Sengoku, and sent to Impel Down. Shiki later manages to escape and begins plotting his revenge on the island of Merveille in the Grand Line. At the same time, many of the events that take place in the current story are beginning, such as the beginning of the Red Hair Pirates and the dawn of the Golden Age of Piracy.
In the New World, at someplace in the sea, the Edd War is about to begin, Buggy freaks out at the potential conflict between the infamous pirates, and asks Crocus if Roger is well enough to fight. Crocus 'assures' him that Roger is perfectly okay. Meanwhile, Shiki asks Roger to join him, hoping to use Roger's information on the Ancient Weapons to rule the world. Roger refuses, not wanting to give up the freedom he has. A battle between the two crews ensues, and a change in the weather allows the Roger Pirates to sink half of Shiki's ships. A side-effect of the battle causes half of a steering wheel to become implanted into Shiki's head.
After conquering the Grand Line and becoming the Pirate King, the Roger Pirates mysteriously disbanded. A year later, news gets out that the Marines have arrested Roger. Furious, Shiki attacks Marine Headquarters and is told by Sengoku and Garp that Roger will be executed in Loguetown, East Blue, as a warning to all pirates. Shiki is infuriated even more that the Pirate King will die in the weakest sea, but Garp tells him that East Blue is also the symbol of peace. A battle between the three erupts, and ends with half of Marineford being leveled and Shiki sent to Impel Down.
A week after Shiki's captured, Roger is executed, sparking the Golden Age of Piracy. All over the world, people have different reactions to the news.
Loguetown: Buggy and Shanks mourn for the loss of their captain while Gecko Moria and Donquixote Doflamingo look eager to watch the execution. Dracule Mihawk, and Monkey D. Dragon seem neutral, while Crocodile's reaction is not seen.
In Impel Down, Shiki is able to escape his cell by cutting off his legs, freeing himself from the seastoneshackles locked there. As news on his escape makes headlines, Shiki replaces his lost limbs with his swords.
On the Moby Dick, Shiki asks Whitebeard if he would like to join him. Whitebeard threatens to kill Shiki if that's all he's here for, to which Shiki says he will lay low for a while, before showing the world what a true pirate is.
On Merveille in the Grand Line, Shiki meets up with his subordinate Dr. Indigo, who has discovered a land of strange, monstrous creatures. Indigo says that the plan will take twenty years to prepare, to which Shiki decides that in twenty years he will show the world what hell is.