Three months after Hanoi's fall, Ai discovers the Cyberse World destroyed and his friends nowhere to be found, prompting him to return to Yusaku. Meanwhile, Yusaku once again fights as Playmaker after the consciousness of the younger brother of his friend, Cal Kolter, is stolen by a mysterious enemy named Bohman. In pursuit of Bohman, Yusaku and Ai are joined by Theodore Hamilton, a victim of the Lost Incident like Yusaku who uses the alias of Soulburner online and Ai's Fire Ignis friend based on Theodore, Flame. Aqua, the Water Ignis, follows soon after by becoming Skye's partner. At the same time, Varis revives Knights of Hanoi to fight against the new enemies. It's revealed that Bohman is a sentient AI created by the Light Ignis, Lightning, who reveals that he's the one who destroyed the Cyberse World and steals Cal's brother's consciousness. Deeming Ignis superior, he decides to destroy humanity. The Wind Ignis, Windy, also assists Lightning after his program was forcefully rewritten. To defeat Lightning's team, Yusaku and his friends join forces with Hanoi and enters Lightning's stronghold. Both sides fights until only Playmaker, Ai, and Bohman are left with the latter having absorbed all other Ignis. Before perishing, Flame and Aqua gives Ai the last of their powers, allowing him and Playmaker to defeat Bohman.
After the fight against Bohman, LINK VRAINS is shut down and Ai disappear together with Yusaku's robot, Roboppi. Replacing LINK VRAINS, SOL Technology develops a humanoid robot SOLtis, which Ai and Roboppi uses to infiltrate SOL Technology and attack its high executive, Queen. Knowing he'll be the next target, Skye's older brother, Akira, enlists the help of Playmaker and his friends as well as Hanoi once more to protect him. Ai and Roboppi manage to defeat everyone except Playmaker, Soulburner, and Varis, who are forced to fight decoys. After defeating Akira and taking over SOL Technology, Ai reopens LINK VRAINS and delivers a message for Playmaker that tells the whereabout of his location. Yusaku confronts Ai alone, leading the two of them to duel. Ai explains that Lightning left behind a simulation that shows the world will be destroyed if Ai is the only Ignis left. Fearing that he'll become like Lightning and Bohman, Ai decides to end his life by either by Playmaker's hand if he lose or by scattering his data into the SOLtis if he win. Despite Playmaker's attempt to dissuade Ai, he still refuses to back down, forcing Playmaker to defeat him. In his last moment, Ai reveals that within the simulations, Yusaku always ends up dying protecting him, which is a future that he wishes to avoid. Months after the final battle, everyone moves on with their lives and Yusaku goes on a journey. Somewhere within the network, Ai is revealed to be alive.