In the aftermath of the battle against Bohman, Yusaku was able to rescue the consciousnesses of everyone captured. However, Ai and the rest of the Ignis did not return, leaving Yusaku alone without his AI companion.
Peace has once again returned to Den City, thanks to the efforts of Playmaker. Ai and Roboppy sneak onto a ship owned by SOL Technologies and attempt to contact Queen as part of their mysterious agenda.
Ai sends a message to Yusaku that he has attacked Queen and SOL Technologies, leaving Yusaku confused about his former partner. Meanwhile, Revolver creates an AI named Pandor to assist him to destroying the last surviving Ignis.
Playmaker has made up his mind to fight against Ai, regardless of the past they have together. While he battles copies of Ai, Blood Shepard and Ghost Girl come across Roboppy, who is ready to prove themselves.
Roboppy continues to give Blood Sheppard and Ghost Girl a hard time, forcing Ghost Girl to summon her new ace monster. Meanwhile, Go Onizuka tracks down the real Ai and begins a duel with him.
Despite constantly being knocked down by Ai's strong monsters, Go is motivated by the kids from his orphanage and keeps standing up using his Gouki cards. Seeing Go's determination, Ai discusses what it feels like to lose one's friends.
As Ai continues to target Yusaku's allies, he makes Akira his next target. Revolver sends Pandor to his aid to prevent the rogue Ignis from succeeding in his goal.
Ai discovers Akira and Aoi in the network and challenges them to a duel in order to gain control of SOL Technologies. Working together, the siblings start to fight off Ai.
Link VRAINS reopens all of a sudden, letting people log in again. Soulburner logs in to try and find some clues about Ai, but instead finds a strange island where Roboppy and a lot of household appliances live.
The battle between Roboppy and Soulburner continues. Soulburner manages to hold off Roboppy's assault, but then the AI taunts him over the fact he was unable to protect Flame.
The battle between Roboppy and Soulburner continues. As he continues to fight, Roboppy thinks back on the nature of his existence and begins to break down.
The battle between Playmaker and Ai continues. Ai overpowers Playmaker with the power of his LINK 6 monster, forcing Playmaker to desperately fight back.
