Ideas for season 3
I figure the season finale aired long enough ago I can start wildly guessing the future based on nothing.
Season 3 will begin a few months later with the crew mostly separated. Zairon successfully copied the blink drive and won the war but Ryo's paranoia over being killed made him put limitation on it; a few ships control the blink drives for the rest of his fleet. Three had his mind wiped again and is now working for the Galactic Authority with Anders. Five's still with Truffault learning more about the corporations and exploring the memories. She isn't being forcibly held but her location isn't known. Two, Six, and the Android are all of the Raza trying to find Three and Five while dealing with the effects of Ryo's war. They managed to capture several blink drives but can't make them work.
The early episode will cover Five rejoining the crew, Three being captured by the crew, and the crew confronting Ryo. Throughout the season Two and Ryo will delve into the cost and responsibilities of being a leader, Six will confront the consequences of the blink drive being used like he wanted, Three will confront his past when the only way to bring him back is to bring Boone back, and the Android will continue discovering herself. And Five will somehow become everybody's shrink because of course she will.