Shattered Seals: During the 20 day period the blood sanctuary seal is not active, a bloodline suppression seal is put on Naruto the locks the security is the disabled state. This was done to hide any bloodline that would give away his parentage before the Hokage was ready. The Hokage did not know about the security seal, as Kushina did not tell anyone about it. Naruto has multiple seals placed on him over time to impair his abilities. The Third Hokage is not aware of all of them, but a tracking seal linked to his crystal ball, a loyalty seal to Konoha, and a compulsion seal to forgive people are placed on his order by Jiraiya. the total number of seals is large. Borrowing from Thundereaper, the main seal array for Kyuubi contains at least 70 seals, one of which hides Naruto's red hair. The other seals will be detailed in the story.
The trigger point is the Forest of Death encounter with the snake sannin. When he applies the 5 elements seal over Naruto's 8 trigram seal, ALL of the seals collapse due to imbalance and interference. Kurama and Naruto are subject to the memories of both Minato's and Kushina's shadow clones. They may also have picked up memories from each other - Kurama will definately get all of Naruto's memories. In the instant all the seals fail, Kyuubi acts to save both of them. A sample of Naruto's genetic material (blood, heart, brain, or whatever) is saved in a personal storage dimension in stasis. The rest of Nartuo's body becomes a living chakra construct like the Biju. The snake may or may not survive what comes next.
Updated to include the Blood Sanctuary Seal information. This seal will survive the ordeal in the genetic sample.