Fort Jinya is first seen in Chapter 7 of Birthright. At the time of this chapter, Sakura and her retainers Hana and Subaki are using the fort as a makeshift hospital for wounded soldiers and citizens. Shortly after the Avatar's arrival, the fort is surrounded by a group Nohrian soldiers, lead by Silas. Sakura stays with the wounded, sending her retainers with Avatar's group to engage the enemy.
Fort Jinya is seen towards the end of Conquest in Chapter 22. The Avatar must seize the fort to continue their invasion of Hoshido, as it is said that the fort is essentially Hoshido's front line. At the time of this chapter, Sakura is healing soldiers in the fort, only to be altered of the Avatar's arrival by Yukimura. Yukimura advises Sakura to retreat from the fort, but she refuses and instead chooses to fight the Avatar.
After the battle, Xander claims the fort for Nohr and gives the Hoshidan army a chance to surrender, promising that they will be spared if they do. Sakura and Yumimura agree to lay down their weapons to Nohr. Hans and Iago then appear to break Xander's promise and start executing Hoshidan troops. The Avatar and Xander both oppose the killing; Xander even threatens to kill Iago. Before Hans and Iago are stopped, Garon enters the scene to overrule Xander and allows Hans and Iago to continue. Sakura sobs as she tries to heal her soldiers but is stopped by Iago, and Yukimura expresses his anger towards the Nohrians.
Shortly after returning from Valla, the Avatar goes to Fort Jinya in hopes of convincing Hoshido to join them in Chapter 8. However, the Avatar has been labeled a traitor to be attacked on site. When the Avatar arrives at the fort, they are met by Yukimura, who orders his guards to capture the Avatar.