How it ends:

I'll quote what he sent me first:

"Here's what's going to happen...

Big super over powered BJ is going to face cognitum, and Cognitum is going to take super over powered BJ's body for herself.  Blackjack is going to get put in a weak flesh and blood body and be forced to face off against Cognitum a second time, completely unaugmented... both to stop her but also to get her baby back.

Happy?"

"Originally I was going to use Boo, but I don't want Boo to die any more.  However, there's another blank that is just perfect for her that I AM going to use: the Blackjack clone made in Hippocratic for her skin grafts.  Blackjack is going to be betrayed by two people she's trusted, be broken and left in Cognitum's old computer.  Dawn, broken and dying from the last confrontation, will help put BJ back in the new body before she dies.  Then Blackjack goes to the moon to confront Cognitum and get her body, and her baby, back.  She succeeded at the former, at great cost, returns to the Hoof for a final showdown with an Awakened Eater of Souls and the Legate."


And according to someone else in the know, Discord is hiding inside Boo and is the one to defeat the EoS.