When news broke that FX's multiple Emmy-winning drama Shōgun was picked up for a second season, it was also revealed that the second season would take place ten years after the events of the first season. The first season of this critically acclaimed show was adapted from James Clavell's bestselling novel of the same name. However, as there is no sequel to the acclaimed novel, the second season represents a wholly original chapter in this series.
This new chapter will take place 10 years after the first season's events in Shōgun, so there will definitely be major changes in the Season 2 story owing to the time jump.
Here's how the massive time jump might affect the story in Shōgun Season 2.
Shōgun Season 2: What will the massive time jump change?

Originally, Shōgun was intended as a 10-episode-long miniseries. Having been adapted from a standalone novel, the series wasn't intended for expansion. However, after widespread critical recognition and the title of the most Emmy-winning television season, it was picked up for another season. The problem with this was that there wasn't any more source material available for this saga.
Co-creators Rachel Kondo and Justin Marks are now forced to create a wholly original new chapter. FX revealed that the new season
"continues the historically-inspired saga of these two men from different worlds whose fates are inextricably entwined."
This would mean that the drama will continue to focus on the connection between Cosmo Jarvis' John Blackthorne and Hiroki Sanada's Lord Yoshii Toranaga, who are confirmed to reprise their roles in the second season. Since the creators continue to use the novel by Clavell as well as the history that inspired it in the first place as the blueprint for the new season, some informed guesses as to what the Season 2 plot might look like can be made.

The ten-year time jump will free the creators from having to focus on the immediate aftermath of Toranaga's win and the build-up of a nation, and instead look at a more developed nation. Toranaga's inspiration in history, Tokugawa, had achieved complete supremacy in every sociopolitical and religious aspect of Japan, a decade after his win. William Adams, on the other hand, Blackthorne's equivalent in history, grew into a trusted advisor and official samurai.
The two lead characters from Shōgun are greatly rooted in historical inspiration. However, some secondary characters, such as Usama Fuji and Toda Buntaro, are less rooted in history, so the creators have complete anonymity over these storylines.
Season 2 might see a much different Blackthorne than the self-serving captain in the first season. Blackthorne might evolve into an even greater asset who respects the Japanese culture and is integrated with it. He might even help Toranaga establish a foreign naval presence and maintain diplomatic relationships. However, whether or not this relationship survives the secret that Toranaga is keeping from Blackthorne about their forced proximity is another story altogether.

Looking at the historical perspective, one possible storyline that might be explored in Season 2 is the military conflict between Ochiba no Kata's historical inspiration, Yodo-dono, and Toranaga's Tokugawa, which led to a siege of Osaka in 1614-15. Season 1 refrained from focusing on the violence, so Season 2 might take the same route and explore complex relationships, political intrigue, and the cultural clashes caused by the conflict instead of the military conflict itself.
Considering no plot details have been revealed about the upcoming season as of now, except the facts mentioned above, only time will tell if any of our informed guesses have any truth to them.
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