I see four (but not limitng to those) options at the moment:
- He stays Captain of the McKenzie, confronts another ship (i.e. the Phoenix, the Alsea or the Achilles) and realizing through that confrontation what is happening, joins the rebellion. That is I think the most ''isolating'' option as it will have you playing alone until this event occurs; then still alone on board your ship interacting with others on their own.
- He may have had his suspicions himself and approached Samji who ''recruited'' him to join the Horizon as the Exec to Redding and commander of the Polaris. That would have you play with me (as Dr Nasaro-Myth) and possibly Redding on board the Horizon Rogers' sister Shelley is also aboard as the bartender if I recall).
- He may have been taken off his command (showing rebellious attitude or not fitting the scheme or getting to close to the truth) and waiting reassignment, volunteer to transfer on the Phoenix as exec. That would have you play with Jeff (Syntron) and me (Livingstone).
- The McKenzie was overtaken by the small crew entirely affected as Jureth was, except for Riker who accidentally escaped the scheme (i.e. because he came back aboard with a shuttle instead of using the transporter). He escaped with one of the two shuttles aboard but it was damaged in the ensuing pursuit and lost adrift in space... until found by one of the rebel ships (your pick; we will work out the specific details later).
The 4th one is my prefered one, as it would give you best flexibility to choose interaction and bring a major clue and direction to the story (getting back his command and adding another LF ship to the rebellion while confronting the scheme directly). But I will not force you into a role. You choose what strikes your fancy, what would be most fun to you. Thus the 5th option is: your ideas

Hope this helps