In Den City, duels are held in the highly advanced VR world Link VRAINS, which is always under attack by the Knights of Hanoi. However, a hero named Playmaker has arrived to face the Knights, capturing a program they want called an Ignis.
Playmaker continues his duel with the Knight of Hanoi using the new Speed Duel rules. Playmaker is backed into a corner by the Knight's Cracking Dragon, but a data storm soon envelopes the field and Playmaker activates his Skill.
Yusaku Fuiki, has become a celebrity in the aftermath of battling Hanoi. He continues to investigate the mysterious program he dubs "Ai." Meanwhile, SOL Technologies begins to look deeper into the identity of Playmaker.
Go Onizuka, a popular duelist on Link VRAINS, accepts an offer from SOL to duel Playmaker. He wants to prove himself and he sees Playmaker as a powerful opponent. He lures Yusaku into a trap and a Speed Duel begins.
Despite taking huge amounts of damage, Go Onizuka keeps fighting and Link Summons his ace monster: Gouki the Great Ogre. Driving Playmaker into a tough corner, he aims to fight back against his strong opponent.
Yusaku meets with Aoi Zaizen, the sister of Akira Zaizen, a higher up in SOL Technologies to gauge their threat. Aoi is a celebrity named Blue Angel who publicly challenges Playmaker to a duel. However, Hanoi lurks in the background.
Blue Angel slowly begins whittling away Playmaker's Life Points using her Trickstar deck. Yusaku manages to fight back and Aoi is forced to use the mysterious card that the Knights of Hanoi gave her.
Aoi is left in a coma after he duel with Yusaku. A grieving Akira lures Playmaker into a trap to get the program to heal her. That's when Revolver, Hanoi's leader appears, and challenges Yusaku to a duel with Aoi's fate on the line.
Revolver gains the upper hand in his battle with Yusaku. Yusaku manages to fight back with his Link Summons, only for Revolver to reveal a shocking Skill.
The duel between Yusaku and Revolver ends in a draw. Being pulled into the center of the Data Storm, Revolver challenges Yusaku to another duel and aims to completely destroy Yusaku's Cyberse cards.
Without his Cyberse cards, Yusaku can only barely hold back Revolver's relentless attack. Summoning his new ace monster, Revolver recounts the origin of Ai and his mission to wipe out all Cyberse from the world.
Yusaku and Revolver keep fighting using the strength of their ace monsters. Despite the odds against him, Yusaku recounts the incident that brought him to this point and steadies his resolve.
Ghost Girl, a bounty hunter who works for SOL Technologies, holds an interview with two reporters recounting all the events that have transpired concerning the evil Knights of Hanoi and the mysterious Playmaker.
Ghost Girl challenges Yusaku to a Speed Duel with some heavy stakes. If she wins, she gets to capture Ai. If Yusaku wins, he gets a window into SOL's server to learn more about the incident that still haunts him.
Even though her One-Turn Kill fails, Ghost Girl manages to put up a good fight against Yusaku. She uses her Altergeist deck to prevent Yusaku from using Storm Access, leaving him with less options to fight back.
Using the program he got from Ghost Girl, Yusaku hacks into SOL Technologies and heads towards the data bank. However, the head chief is onto him and sends two powerful AIs to halt his progress.
Blue Angel arrives to assist Playmaker in battling the AI duelists halting his progress. Even though Yusaku is forced to discard his entire hand in one turn, he refuses to give up until he learns the truth.
Playmaker arrives in the center of SOL's server only to encounter Akira. Having learned of the events that occurred ten years ago, he duels Playmaker to stop him from learning the truth.
As Playmaker and Akira keep dueling, the true nature of the Lost Incident is made clear. After being kidnapped for 6 months and forced to a duel, Playmaker won't stop until he gets his revenge on those responsible.
Despite Akira's impassioned pleas, Yusaku will not abandon his quest for revenge. If he wants to finally learn the truth, he will need to break through Akira's Tindangle deck.
Playmaker learns that avatars in Link VRAINS are being turned into agents for Hanoi, leaving their bodies comatose. Onizuka, losing his friend to this process, tracks down the one responsible.
Go Onizuka fights Dr. Genome, the head of the Another project, with Playmaker's identity on the line. Against Genome's Helixx deck, the honorable Onizuka suddenly puts on a new persona.
Even with his heel persona of Dark Mask, Onizuka has trouble fighting against Genome and winning the anti virus program. When all seems lost, Playmaker arrives to encourage Onizuka to fight.
Aoi stands at a crossroads, unsure of what she wants to do with her life. Logging into Link VRAINS as Blue Angel, she encounters Baira, the creator of the Another virus.
The duel between Blue Angel's Trickstar deck and Baira's Dark Mummy deck continues. Baira begins infecting Aoi's deck with virus cards while Yusaku and AI research the Another program.
Naoki Shima, one of Yusaku's classmates, is inspired by Playmaker and decides he wants to be a hero. With data from a Cyberse card, he logs into VRAINS to face Hanoi as Brave Max.
Faust, a high ranking commander in the Knights of Hanoi, kidnaps Naoki to lure Playmaker into a trap. Playmaker arrives to fight Faust as a Speed Duel begins.
Preparing for the worst, Kusanagi writes a report detailing the battles between Playmaker and the Knights of Hanoi. Revolver then decides it's time for Hanoi's final gambit.
Despite peace having returned into Link VRAINS, Yusaku suspects something and logs in. Working with Ghost Girl, they sneak into a base and discover Revolver.
Revolver and Ghost Girl continue their Speed Duel as Yusaku is chased by data monsters. Despite Revolver's overwhelming power, Ghost Girl fights back with all of her strength.
Revolver's ultimate plan, the Tower of Hanoi, begins to absorb all the data in Link VRAINS. In 6 hours, it will detonate and delete all computer data. Yusake and his friends scramble to stop Hanoi once and for all.
