As the game progresses, the hostilities between the Youth League and New Yevon build to a head. In the meantime, the Gullwings discover an ancient sphere containing images of an enormous machina weapon called "Vegnagun" that was secretly buried beneath the city of Bevelle. The weapon has enough power to threaten all of Spira,[7][8] and, moreover, it is revealed to the player that Vegnagun is unable to distinguish friend from foe once activated.[9] The Gullwings then join forces with the Leblanc Syndicate to investigate the underground areas of the city in an attempt to destroy the machine before it can be used by either side in the upcoming conflict. However, discovering a large tunnel recently dug into the floor of the weapon's chamber, they realize that Vegnagun has apparently been moved to the Farplane, located at Spira's core.
Disagreements between Spira's factions are soon punctuated further after the disappearance of Baralai, Nooj and Gippal — the leaders of New Yevon, the Youth League and the Machine Faction respectively. Returning to the underground areas of Bevelle, the Gullwings discover the missing faction leaders discussing Vegnagun and learn that the machine's artificial intelligence allows it to detect hostility and to respond by activating itself and fleeing.[10] Additionally, it is revealed that Nooj had come to Bevelle with the intention of destroying Vegnagun previously, prompting it to flee to the Farplane.[11] The player then learns that Paine had once been friends with all three men, assigned to be their sphere recorder while they were candidates for the Crimson Squad, an elite group intended to be assigned leadership of Crusader chapters across Spira.[12]
Two years earlier in a cave beneath Mushroom Rock Road called "the Den of Woe", just before the failed Operation Mi'ihen, the squad's final exercise was conducted. Within the cave, the various squad candidates were swarmed by pyreflies and driven to kill one another. The only survivors were Paine, Baralai, Gippal and Nooj, who were themselves targeted by the Yevon order afterward when they revealed having seen images of Vegnagun while in the cave. Soon after, Nooj shot his surviving comrades and left them to die, severing the friendship the group had with one another. However, at this time, it is revealed that he was not acting of his own accord when he shot them. The feelings that drove the squad members to kill one another are revealed to have been the despair of the game's antagonist, Shuyin, who died 1000 years earlier.[13] Before the four survivors could leave the cave, the spirit of Shuyin — requiring a host in order to interact with the world physically[14] — had possessed Nooj, and later forced him to shoot his comrades.[15] In the time since, Shuyin had been subtly goading Nooj on a subconscious level, coercing him to approach Vegnagun so that he could use Nooj's body to control it.[16]
A screenshot of Yuna's concert, which prompts the memories of Lenne to emerge from the Songstress dressphereNooj's will was too strong for him to be completely controlled, and his desire to destroy the large machina prompted it to flee.[17] Now desiring a new host, Shuyin leaves Nooj's body and possesses Baralai's, pursuing Vegnagun to the Farplane. Nooj and Gippal follow in pursuit, asking Yuna to keep things under control on the surface. In doing so, the player must fight and defeat each of Yuna's aeons from Final Fantasy X, their spirits now corrupted by Shuyin's despair on the Farplane.[18] During this mission, Yuna falls into the Farplane and meets Shuyin, who mistakes her for a woman named "Lenne". Feeling affection toward him that is not her own and finding herself unwilling to move away from him, she listens as Shuyin describes how he "awoke" after he had died, alone and unable to find Lenne. He then expresses anger that Spira's citizens have not yet come to understand the heartache that war can cause, and reveals that he has developed a plan to use the old, but still operational Vegnagun to destroy all of Spira, ending the possibility of there ever again being a war. In so doing, he believes that he will be making the world a better place.[19]
The player learns that 1000 years before the game, Shuyin was a famous blitzball player in the high-tech metropolis of Zanarkand, and the lover of a popular songstress and summoner — Lenne. Shuyin's memory would then form Tidus in Dream Zanarkand in the events of Final Fantasy X. The two lived during Zanarkand's war with the more powerful Bevelle, and during the course of the war, Zanarkand ordered all summoners to the front lines, separating the couple. Believing that Lenne would die in battle, Shuyin decided that the only way to save her was to infiltrate Bevelle, commandeer Vegnagun, and use it to destroy Zanarkand's enemies. However, Lenne perceived Shuyin's intentions, and — unwilling to allow him to take the lives of many others for her sake — followed him.[20] When she caught up to Shuyin in Bevelle, he had only just begun to operate Vegnagun's control panel, an organ integrated into its head. Before he could use the giant cannon located in its mouth to destroy the city, Lenne asked him to stop. Shuyin did as she asked, but a group of Bevelle soldiers arrived a moment later and shot the couple. Fatally injured, Shuyin failed to hear Lenne saying that she loved him before they died.[21]
Over the course of the following 1000 years, Shuyin's despair and resentment over his failure to save Lenne bonded to pyreflies and caused him to constantly experience the anguish of that moment.[22] Over time, his despair became so powerful that it began acting on its own,[23] and he came to believe that — in addition to helping the world — he would fade away with Lenne if he destroyed Spira.
Now with an understanding of Shuyin's hatred for war, Yuna manages to return to the surface and the Gullwings organize a concert to which everyone in Spira is invited, supporters of the Youth League and New Yevon alike. Additionally, the Songstress dressphere worn by Yuna is revealed to be comprised of Lenne's memories, resulting in a sphere screen projecting them to everyone in attendance during the concert. Witnessing images of Shuyin and Lenne's last moments, Spira's citizens begin to understand the unproductive nature of their disagreements. The player then learns that it was because of Lenne's memories that Shuyin had mistaken Yuna for Lenne and she had felt affection toward him.[24]
Tidus and Yuna reunitedAlthough the factional fighting has ceased, Shuyin has nearly carried out his plan to use Vegnagun's cannon to destroy the planet from beneath its surface. Joining forces with the Leblanc Syndicate once again, the Gullwings make their way to the Farplane and find Gippal and Nooj already battling Vegnagun. Working together, they manage to disable the giant machina before its cannon can fire at Spira. Finally confronting Shuyin, Lenne's consciousness emerges from the Songstress dressphere and convinces him to abandon his mission and be at rest. Thanking Yuna, Lenne guides Shuyin's spirit to peace on the Farplane.
Subsequently, the fayth once located in Bevelle appears before Yuna and thanks her as well. He then asks her if she would like to see "him" again. Should the player reply "Yes" — and a sufficient percentage of the game's optional storyline has been completed — the fayth locate Tidus' scattered pyreflies and send them to Besaid, where they reform. Thus, when Yuna returns home, she is reunited with Tidus. Players who achieve 100% completion see an additional reunion scene in Zanarkand.
