NOTE: This chapter primarily serves as a section divider and an introductory chapter, feel free to skip to the story if you're not interested in the small details.
Year 850: The Escape from Stohess,
After struggling through months of indecisive internal conflict; being torn apart between two worlds, you finally chose to side with Annie. This as with any choice, comes with great consequences.
Having made an enemy of both Marley and Humanity inside the Walls, you're forced to improvise and come up with a plan to clear your names and earn humanity's good will once more. To that end, you and Annie embark on an adventure that unbeknownst to you— is sure to change the greater course of history.
CLARIFICATIONS: Since you and Annie's escape from Stohess overlaps with Zeke's attack as well as Reiner and Bertolt's subsequent escape, this will hopefully clarify the order in which the events take place and clear any doubts. I've included a map in Chapter 03 which will hopefully clarify things further.
01. In the canon timeline, after their escape, Reiner and Bertolt meet up with Zeke in Shiganshina where they camp out for two months. In this timeline, they don't stop at Shiganshina and instead, head straight to the port where they meet up with Zeke and sail back to Marley. There, they take some time to spend with their families and rest before coming back in time to ambush the Survey Corps.
02. The reason you don't run into Zeke is because he wasn't there when Annie, Reiner and Bertolt broke the gate in Shiganshina five years ago. It meant that at the time, he doesn't know about the breach in the walls, so he takes a different route and climbs over Wall Maria from the west.