Act III:

-I was thinking about skipping forward about six months. I know that's a long time, but I feel like it would not only give Ari and Yerbol to teach at the academy, but also for Manus and Jean to establish their network. 

-During this six month period, Manus and Jean will be working behind the scenes with their group of Force users who don't believe in the Qyaari's diplomatic approach. Staying out of sight, the former Jedi Masters establish a new order called The Faceless(work in progress on the name!) that stress each member is tied to the other by the Force. Not only are they tied together, but each must harness their abilities to become one with the Force as living weapons, defending the "sanctity" of the Force from those who cannot "comprehend it". So, in other words, they hate anyone who can't use the Force or don't use it the way they want. 

-Different from the manipulation of Bracknell and the chaos of Illesia, Manus and Jean desire to carve out their own niche on various worlds, establishing underground teaching facilities that train remaining Force users in their philosophy in order to stay as isolated from the galaxy as possible. This isolationist perspective is shattered when Manus scouts out Belsavis as a training facility, seeing as the Alliance has abandoned the planet in favor of more isolated worlds for their most dangerous criminals. He discovers an underground network pf passages that eventually lead to a temple forged by Rakata who claimed to be enemies of the True Sith. They too believed in the power of the Force and left behind their teachings. Manus brings back their teachings to Jean and establishes a base of operations on Belsavis while settling on a course of action: take down the Qyaari before they can spread their message of harmony to other Force users. 

-Manus and Jean begin to orchestrate small attacks on Alliance supply convoys headed to Zinuthra, which would naturally draw out the Qyaari. It is there that The Faceless begin to capture the younger squadrons sent to investigate, dedicated to turning them to their cause. After a few of these strikes, Manus and Jean get bolder, sending out squadrons to attack budding Qyaari settlements on other worlds. This leads to Yerbol and Aria being sent to...well, some planet with a Qyaari settlement, to thwart the attackers. 

-From there, we can have the duo capture one of the attackers and interrogate them? Or maybe interrogate them on site? Or find some clue on a body as to where one of the Faceless bases are? 

That's what I've got so far...what do you think? I tried to fit Quesh in based on your ideas, but had a hard time. How do you think we could fit it in?