Hanoi Project

The Hanoi Project (ハノイプロジェクト, Hanoi Purojekuto), also known as the Lost Incident (ロスト, Rosuto Jiken), is an event that occurred 10 years prior to the start of the Yu-Gi-Oh! VRAINS anime. Kiyoshi Kogami, a researcher at SOL Technologies, developed and executed the incident without the knowledge of his company. This project resulted in the creation of the Ignis.

History
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 and was able to complete the Ignis before the company infected him with a computer virus to cover up the incident. Furthermore, Dr. Kogami tests several simulations of the Ignis growth and eventually concludes that their continuous development would cause them to supervise and eventually destroy humanity, forming the Knights of Hanoi with his assistants to kill his own creation.

The project's name is the main reason why Yusaku and Kolter suspect the Knights of Hanoi of 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 Takeru work with their Ignis to support co-existence between human and Ignis, Jin is currently being controlled by his Ignis Lightning and serves as his puppet, Specter chose to serve under the Knights of Hanoi as Ryoken's right-hand man in the fight against the Ignis, Miyu is currently comatose after being infected with a computer virus by Lightning, and Windy caused his partner to be involved in a reckless driving accident.

Researchers

 * Kiyoshi Kogami
 * Clarissa Turner
 * Aso
 * Dr. Genome
 * 3 additional unnamed assistants

Victims
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 Spectre was able to detect that his Ignis Earth got terminated.