Hey everyone, I'm a relatively new DM with something of an AMBITIOUS project. I currently run a Sci-Fi/Cyberpunk/Fantasy mixed campaign with a bunch of irl friends of mine as the PC's. Its a big project and personally I have never done something like this before. I have a solid setting and timeline and all that but right now my concern is the campaign itself. 

For context, heres a little explanation of the current situation. My party, a band of misfits from all over the galaxy, has been recruited by an extremist augment rights movement to help expose a plot to destabilize the city of District 1, and eventually the entire Galactic Alliance (Elves, Dwarves ,Terrans, etc.) But an obstacle is in the way: Alozar Odysseus, CEO of Lazarus Corp. Lazarus Corp has been hunting down the party and members of the Extremist organization to try and stop them from uncovering the truth. Needless to say eventually the party reached Lazarus HQ, and of course attempted to face down the CEO himself (Which is the current BBEG). Long story short its a trap and the whole operation gets completely screwed over. This eventually leads to Lazarus using its influence on the police to make the Party wanted, sending them off on the run. They made contact with an officer of the extremists who was to re-assign them back to the Alliance homeworld to draw up a new plan... Heres where my problem comes in.

Yosef... Bloody freakin Yosef... Yosef is a Tabaxi PC who drinks a lot and generally puts his self preservation before everything else (Which is fine) but Yosef deadass tells the officer to basically go screw himself and with a few failed checks and saves lets just say the Extremists refuse to associate with the party anymore and they are once again on the run.

Now my plot is completely derailed. Not that it was entirely on rails but I did not plan for this. I have no idea how to carry on the plot. So im in a bit of a tight spot and wouldnt mind some advice from veteran DM's.

"Carry on the plot" is your rail.  They're off it now.  It sounds like you've developed enough of a world for the characters to move on within.  And you've reached what I think is the really cool part of game world development where it's now a "shared" thing between the DM and PCs.  You get to let go a lot.

According to the original script, the character were apparently going to somehow save a world or advance the cause of augment rights or whatever.  They are no longer in position to do so. So what happens in the world if they had failed in the script?  That's your new world, and they have to react to it until they find themselves in a drivers seat again, which may make time as new world orders shake out.  Maybe the augment rights groups have a plan B, or a last stand the PCs can get involved in, or the world just got a lot darker for everyone on that side (including the PCs?).  You now have a more open world for a band of fugitive mercenaries to explore while being hunted or hiding on your world's frontiers ("If you have a problem, and you can find them, maybe you can hire the A Team").  Generate some stock hunters (maybe a fleshed out NPC for the Space Marshal or Security Sector Agent or bounty hunter tasked with dealing with the loose end of the PCs), and mix them in with some more garden variety merc work (some of which may reintegrate them into the Augment cause if they're still around after the fail) until things are fleshed out to try another arc (which may lead into the original arc or go elsewhere).  And have role play consequences.  Maybe in making a mess of things they're support system has turned their back on them.  Their contacts will at best reluctantly work with them or burn any association because of not just their failure but the risk of the association.

I actually really like this idea! I have to put some of this into consideration. The idea of sharing the world actually feels really nice. Thanks!

Your party is currently on the road where both fractions don't want to work with the party. That is a road. I would say let them run that one for a while, hunted down by the police and give them no rest. Make them suffer a bit for the choiche the Tabaxi made.

All you have to do next, is prepare multiple paths that lead to new roads. If the players want to single handedly defeat the Lazarus Corp? Let someone inform them over an ancient hidden spacestation that they could use as a base. The space station has shields that can not be detected by the Lazarus Corp. Only problem that it is currently invested by mindless killer drones... 

If they want to gain the trust of the Extremists once more? They catch an emergency broadcast of a small Extremist team, stuck in a spatial rift, hunted down by evil twins from an alternate dimension. Your team can save all of them and one of the teammembers turns out to be the heir of the Extremists leader. Now the party is once more back in alliance with the Extremists.

Or perhaps the party wants to eliminate the Extremist Officer and take control over the Extremists. Fortunately enough they know a guy who sells terraformers to the officer and this guy can smuggle you to his planetary home. If your paty manages to evade the security and hired muscles, you stand once more eye in eye with the Officer. The party can intimidate him then to continue, or kill him, or let them be creative.

All you have to do is give the players a couple of opportunities and let them pick where they want to go. Does this help?

It very much does! thank you!