Are you asking about Prophecy or Secret Ops? Prophecy has alternate missions and some alternate systems. Secret Ops sends you to the same systems, but there are definitely alternate missions and paths within those systems based on how you perform. You can see how this works at https://www.wcnews.com/guides/
Secret Ops works mostly the same as Wing Commander Prophecy, where there are occasionally 'losing' serieses but moreso there are individual mission that can split... and it can get pretty complex! For instance, you fly five missions in the Talos System but there are eight total. Which ones you get to are determined by individual objectives.
Thanks for the link, I mean Seceret Ops. Does it have a loosing path that you can end up on early so you never get to the last mission and is there a clear cut win or loose ending? Is there a way to invert the mouse so it acts like a flight stick? Pulling back is climb and pushing forward is diving in other words? Having it the other way makes it impossible to play
My recollection of Secret Ops' episodic mission design is that there are 'winning' and 'losing' paths within each episode/system, with the main exception being the penultimate episode which can be in either Krieger (winning) or Sirius (losing) systems. As Chris mentioned there are opportunities to win - or lose - right up until the final mission in Proxima.