Peace has been restored to a new Link VRAINS despite Playmaker being a fugitive. AI discovers the Cyberse World destroyed while elsewhere a mysterious figure appears before Yusaku and Kusanagi.
Yusaku continues to chase after the mysterious Bohman, who stole the consciousness of Kusanagi's brother. Bohman plays a Link Spell that gives him a strong advantage over Yusaku.
The enigmatic Soulburner and Flame appear to face Bit and Boot while Yusaku continues to chase Bohman. As Bit and Boot fuse, Soulburner fights back with his Salamangreat deck.
Transfer student Takeru Homura reveals that he is Soulburner to Yusaku in the real world. He is allied with the Fire Ignis Flame and is a survivor of the Lost Incident. With the Cyberse World gone, they discuss an alliance.
Playmaker and Soulburner follow a lead in Link VRAINS only to encounter Go Onizuka. Having sacrificed everything to become a bounty hunter, Onizuka demands to fight Yusaku only for Soulburner to intervene.
Go Onizuka continues to attack with his army of Dinowrestlers. Brokenhearted by seeing his hero like this, Soulburner recalls the Lost Incident and how it changed his life in more ways than one.
Just as Playmaker was about to reach the gate, he encounters the bounty hunter Blood Shepherd. Hired by SOL to hunt Playmaker and Ai, as well as fueled by a hatred of AIs, Blood Shepherd attacks Playmaker with his Battledrones.
Blood Shepherd continues to negate every move that Playmaker tries. When even Storm Access fails, Blood Shepherd reiterates his distrust of AIs. Yusaku and Ai have one final trick up their sleeve however.
Playmaker and Soulburner enter the gate and appear in a mysterious world where they encounter the Wind Ignis, Windy. Unbeknownst to them, Ghost Girl and Aoi, now called Blue Girl, are following them.
Blue Girl and Soulburner begin their duel. Blue Girl does not really understand the nature of the Ignis and attacks with her upgraded Trickstars. Meanwhile, Playmaker continues to pursue Bohman.
Being given new memories by his benefactor, Bohman starts another duel against Playmaker with Jin's consciousness on the line. As Hydradrives and Cyberse collide, Bohman reveals some shocking information.
Bohman claims that he is the real Yusaku Fujiki and that Playmaker is just a copy. As Playmaker and Ai ponder his claims, they continue to fight back against Bohman's Hydradrive strategy.
The Knights of Hanoi, thought disbanded, now decide to reunite to face a new threat. Revolver, allied with Specter, Faust, and Genome, aim to rescue to their comrade Baira.
Soulburner falls into the trap set by Blood Shepherd. As Yusaku contends with two bounty hunters, Blood Shepherd sifts through Soulburner's memories, including how he met Flame and the trauma from the Lost Incident.
Ghost Girl and Aoi research Playmaker's identity and come to the conclusion that Brave Max, aka Naoki Shima, is a good lead. Meanwhile, Playmaker ponders the true nature of his new enemy.
Playmaker continues to duel Kenmochi and Yoroizaka. Soulburner wakes up and begins a duel with Blood Shepherd. Shepherd's AI begins to explain the effects of all his cards, but that is only one piece of a devious plan.
Blood Shepherd summons three copies of the monster that traumatized Soulburner. However, Soulburner had already faced his fear and performs a never before seen Reincarnation Link Summon to counter.
Takeru becomes fascinated by Kusanagi and Yusaku, questioning how the two of them met. Kusanagi explains that his brother's trauma led him to investigating the Knights of Hanoi, which led to a chance meeting with Yusaku.
In the past, Kusanagi and Playmaker agreed to team up to fight the Knights of Hanoi. Learning of a powerful deck of Cyberse cards, they travel to a pyramid in Link VRAINS to acquire their trump card.
Decoding a secret message on a forum, Yusaku and Ai discover the Earth Ignis, whom they dub Earth. Earth is not keen to trust humans based on what the Water Ignis said and tests Yusaku through a duel.
Armed with G Golem Crystal Heart, a card belonging to the Water Ignis Aqua, Earth continues to fight Yusaku. Hoping to convince Earth to join their side, Yusaku and Ai fight back fiercely.
Ai is lured to a strange website where he encounters Windy and the Light Ignis, named Lightning. Lightning reveals that he has been the mastermind behind everything, hoping to supplant humans so the Ignis may rule.
Revolver comes to the aid of Playmaker, much to his shock. However, he is only here to accomplish his own mission of wiping out the Ignis once and for all. Thus he begins a duel with Windy.
The duel between Windy and his Stormriders and Revolver and his Rokkets continues. Windy gleefully reveals that he killed his partner and doesn't trust humans. A cold Revolver then does something unexpected
Lightning reveals that he stole Jin's consciousness and declares war with the human race so that Ignis may prevail. As they flee, Yusaku attempts to give chase only for Bohman to challenge him to another duel.
Bohman and Yusaku continue their duel. Bohman reveals his true purpose as a next generation AI who will be the first in a new line. His goal at hand, Bohman continues his assault.
The battle between Bohman and Playmaker continues. Bohman uses Storm Access to acquire a Link 4 monster and dominate the field. Ai then reveals he has a plan to win the duel.
Earth manages to locate Aqua, who was imprisoned by Lightning, and frees her. However, as they flee, Go Onizuka appears to capture the two Ignis for SOL Technologies, beginning a duel.
Having saved Aqua, Earth continues his desperate battle with Go Onizuka. Enfused with an AI and a thirst for revenge, Onizuka begins a wild attack. Yusaku and the others hurry to where the Ignis are.
SOL had captured Earth while Aqua was able to escape. Blood Shepherd is sent to hunt down Aqua, only to encounter Ghost Girl. Aoi discovers Aqua and learns about a secret connection that they share.
Ghost Girl tries to stop Blood Shepherd from going after Aoi by dueling him. With both of their accounts on the line, the siblings battle while unspoken words linger in the background.
Blood Shepherd continues with his goal on purging the Ignis for SOL. Revolver appears before him and offers an alliance, which Shepherd rejects. Chastising his recklessness, Revolver challenges him to a duel.
Lightning perceives that his enemies are growing too quickly. He lures Blood Shepherd into a trap with the intent of adding him to their ranks. The defiant Blood Shepherd accepts his challenge and a duel begins.
The duel between Blood Shepherd and Lightning continues. Armed with Judgment Arrows and his Armatos Legio deck, Lightning resumes a brutal attack on Blood Shepherd's drones.
Akira suspects that SOL has too far with fusing an AI into Go Onizuka's body. Armed with only his anger, Onizuka challenges Playmaker to a duel so that he can have his revenge once and for all.
Having absorbed Earth into himself, Onizuka uses the power of Crystal Heart and his Anti-Skill to push Playmaker into a corner. The odds are stacked against him as Yusaku and Ai make a move.
Revolver invites Yusaku and his allies to a meeting to discuss the Ignis situation. He offers a team-up, but Soulburner cannot forgive Hanoi for the Lost Incident and lashes out at Revolver.
After Revolver accepts the responsibility for Soulburner's trauma, the gang agrees to a truce. They start heading to Mirror Link VRAINS, where Lightning's faction is gathered.
Haru is tasked by Lightning to face Blue Maiden. Burdened by thoughts of his fake brother, Bohman, Haru appears before the group. Aoi and Aqua face him together in Blue Maiden's first duel.
As the gang gets separated, Lightning appears to duel Specter, whom he seems the weakest of the group. The deranged Specter accepts his challenge and a duel begins.
Specter manages to steal Judgment Arrows and reverses Lightning's Extra Link. As Specter gloats about the power of Hanoi, Lightning's ice calm demeanor suddenly shatters.
Windy, who is still bitter about his loss, challenges Soulburner to a duel. Belittling the power of teamwork, Windy and his Stormriders start an attack on Soulburner and Flame.
The duel between Windy and Soulburner continues. Mocking the idea of humans and AI working together, he unleashes his ace monster. Soulburner and Flame are ready to prove him wrong and they counterattack.
Bohman appears before Blue Maiden, explaining how it is his destiny to create a new generation of AI. To stop his plans, Blue Maiden challenges him. However, Bohman is weirdly calm despite losing his brother.
Bohman and Blue Maiden continue their duel. Bohman continues to evolve and grow stronger, unleashing his Hydradrives. Nevertheless, Aoi and Aqua refuse to give up
Lightning realizes he is at a disadvantage and contacts Kusanagi. Using Jin's life as leverage, he orders Kusanagi to duel against Playmaker. The former allies have no choice but to fight.
To save his brother, Kusanagi uses his knowledge of Yusaku's deck to completely lock down his moves. Yusaku is not eager to face his partner and friend, but cannot back down from Lightning's tricks.
Playmaker passes out after his battle with Kusanagi. Meanwhile, Bohman appears before Soulburner and Flame, hoping to add the Fire and Wind Ignis to his power. An angry Soulburner accepts his challenge.
The duel between Bohman and Soulburner continues. Despite everything going on, Bohman's bravado will not waver as he taunts Soulburner. Refusing to give him, he and Flame plan a counterattack.
Revolver encounters Lightning, who has been watching all of these events unfold. Challenging Lightning to a duel, Revolver decides to reveal Lightning's secret sin that sends him into a fit of rage.
