Question: What happens at the end of Kali yuga to all those souls that have not yet realized God?
Answer by Romapada Swami: According to Srimad Bhagavatam, 12.2.20-22, the normal course of Kali Yuga ends with Kalki Avatar annihilating the millions of souls who masquerade as kings; these souls receive sayujya liberation, or a state of sinlessness, but their devotion to the Supreme Lord still needs to be awakened. The remaining souls are uplifted by the Lord’s presence, they become transcendentally purified, and they come at once to the platform of goodness. These souls assist in populating the planet with other elevated souls, thus playing their role in ushering in the Satya Yuga.
In Chapter Four of Canto 12, we find a detailed description of what happens and the end of the Kali Yugas that come at the end of Brahma’s day (i.e. after 1,000 yuga cycles are completed), as well as the end of Brahma’s life. The basic idea is that the souls are held in a dormant state, with no manifested activities or forms, and they remain in that condition until the next creation takes place.