See, this is what I'm saying. There can't be a next that has any logic when your plot is based on what seems to be a fundamental misunderstanding of one of your main characters. You can write it from the imperial pov, but you have to write Shan's actions and words from a jedi one. so you need to know what that is. And I'm not saying that you shouldn't have a rough outline, but you can't make decisions about what what characters would do until you really know them. The fact is, that often changes during writing as well.
Why? If you don't like the Malgus&Satele part, just ignore it. SI captured her son and lured her there. Then she chose to be captured by the SI to gain her son's freedom, that fit her character well right? Then can you give advice of what would happen next?
But if you still want to continue on the Malgus pair, like I said, she could aid her ancestor's plan of wipe out 98% of the Imperial population, work with a Sith Lord who had killed countless Jedi and betrayed her ancestor, caused the death of a savior of the Jedi order and her ancestor to be imprisoned by the Emperor for 300 years. The Jedi under her leadership framed someone with a lot of crimes that even the chancellor said it was wrong. Why do you think it's impossible for her to use Malgus to have a child? Her personal hatred?