Yu-Gi-Oh Head Canon: The people of Kul Elna were still alive when they were smelted into the Millennium Items.
The Millennium Tome called for 99 human sacrifices in order to create the seven Millennium Items. Not only did this call for their blood, bones, and flesh to be smelted into the gold that created them but the souls of the people were needed to give the Millennium Items their magical properties. To accomplish this, Akhenaden had them sedated so they wouldn’t struggle and dropped them in one by one as Bakura watched them drown and burn to death in the metal.
(Alternative head canon is that the medicine used for sedation was opium. Being a powerful drug that allowed for Egyptians to perform surgeries, it was the perfect choice and allowed for the victims to stay alive long enough for their inevitable demise. A terrible twist, however, is that opium is also a well known ingredient in morphine, which is a well known treatment for chronic pain. So, if any of the victims were “lucky”, the agony they felt may have been lessened by the effects of the opium.)
(This head canon is only supported by the Japanese anime. If you listen closely, you can hear the screams of the victims coincide with the bodies dropping in.)
Two souls were both two sides of the same coin. Descended from mixed Egyptian and Greek blood, Judai and Johan were born with the abilities to see spirits. Judai can look at a person and see if their Ka has been infused with dark monsters and Johan with light. During Atem’s Father’s reign as Pharaoh, Judai was a prince that was taken captive as a prisoner of war, Johan his guard. When his father died, Atem could see their potential and offered them sanctuary in his harem. Judai took that sanctuary and Johan as well on the condition that he was to be Judai;s personal guard.
Because he can see the dark spirits within people, Atem gifted him the Millennium Key.