The Hanoi Project (ハノイプロジェクト, Hanoi Purojekuto), also known as the Lost Incident (ロスト
10 years before the present, Dr. Kogami believed humanity would eventually become extinct since human life always ended in death or due to phenomenons. He sought to create humanity's successor---AI with free will. Together with Clarissa Turner, Aso and Dr. Genome, Dr. Kogami planned and executed the Hanoi Project, kidnapping six children one-by-one. During their six months of captivity, the children were imprisoned separately in rooms with nothing but VR equipment. Believing that Duels were the best way for AI to understand humans, Kogami forced the six children to Duel in a virtual arena where if they did not win, they were electrocuted and starved. Behind the scenes, the scientists used the Duel data to create the Ignis, who were modeled after the six children and the Duel Monsters' Attributes. After the children were rescued, the incident was covered up.
In the aftermath of the incident, several of the children suffered from post-traumatic stress disorder, with some taking years of therapy to recover while others have not recovered at all. During the final showdown between Playmaker and Varis, the latter revealed he was the one who reached out to Yusaku. He couldn't stand hearing the pain of the six children so he called the police. Once the incident came to light, Dr. Kogami was imprisoned by SOL Technologies but was able to complete the Ignis before the company covered up the incident. During the subsequent three years, Dr. Kogami tests several simulations of the Ignis growth as a whole and eventually concludes that their continuous development would cause them to eventually destroy humanity. Before Kogami can deduce Lightning as the cause, Lightning infected him with a computer virus, rendering him comatose and causing SOL Technologies to declare him physically deceased. After Varis revives Kogami in the network world, Kogami forms the Knights of Hanoi and decides to destroy his own creation before they harm humanity.
The project's name is the main reason why Yusaku and Kolter suspect the Knights of Hanoi have a major involvement in the incident and thus why they pursue them. Varis confirmed his knowledge of the incident during his Duel with Yusaku, while Dr. Kogami, Clarissa Turner and Aso were all present during the incident, watching the victims' suffering.
10 years later, some of the victims were reunited with their Ignis. Yusaku and Theodore work with their Ignis to support co-existence between human and Ignis, Jin was saved from Lightning and relieved of his trauma, Specter chose to serve under the Knights of Hanoi as Ryoken's right-hand man in the fight against the Ignis, Miyu Sugisaki was saved from her comatose state after being infected with a computer virus by Lightning, and Windy (whom Lightning brainwashed) caused his partner to be involved in a reckless driving accident.
The victims of the Lost Incident each have a special connection to the Ignis they're associated with, as seen with Yusaku and Ai's Link Sense and when Specter was able to detect that his Ignis Earth got terminated.
|Victim||Effect||Status||Ignis||Attribute||Age by the time of abduction|
|Yusaku Fujiki||Post-traumatic stress disorder, grew a strong desire for revenge, 'time stopped moving' for him, his heart was closed off.||Active||Ai (Unknown)||DARK||6|
|Jin Kolter||Heavy post-traumatic stress disorder, 'closed his heart' from the world. All of his memories of the Lost Incident were erased after Lightning converted a portion of his consciousness into extra LP.||Active||Lightning (Deceased)||LIGHT||6|
|Specter||Started enjoying life, 'time started moving' for him, grew to distrust humanity.||Active||Earth (Deceased)||EARTH||Unknown|
|Theodore Hamilton||Became socially reclusive, suffered severe trauma towards the monster "Despair from the Dark", 'time stopped moving' for him due to his parents' death.||Active||Flame (Deceased)||FIRE||6|
|Miyu Sugisaki||Endured through the project by her strong resolve to see Skye again.||Active||Aqua (Deceased)||WATER||Unknown|
|Unnamed boy||Specific effects are unknown. But later made friends and regained a sense of hope in life. Involved in a car crash instigated by a brainwashed Windy.||Unknown||Windy (Deceased)||WIND||Unknown|
- Yusaku and Specter are the only Lost Incident victims to have Dueled against each other.
- Yusaku is the only victim whose known Deck is not solely comprised of monsters that are that of his Ignis' corresponding Attribute (DARK).