Timothius:
**** MICHAEL
Katy gets incapacitated (Sick or hurt bad) and it's up to Mike to take care of the Freedom Fighters.
That is definitely possible. Could also tie it in if you wished with a mission to get something to treat Katy's condition (could be a type of poison or something.)
Timothius:
**** SAMUEL
Samuel betrayal story arch
Samuel has a chance to betray and does not?
One of Sam's crew rescued?
Someone from Stelaris gets shot down (Or lands?) only for Samuel to discover it was a space pirate who stole a Stelaris ship.
Well fir the first one/two, there are a number of factors that would come into play as Samuel doesn't trust Robotnik or anyone who works for him, thus who Samuel would even be tempted to consider such an act given how it burns bridges behind him.
Since Samuel's three crew members have been roboticized, rescuing one would be difficult.
A stolen Stelaris ship being encountered could be troubling, especially if it is in the hands of pirates. Stelaris and any other major interstellar organization the pirates could steal from would have access to teraforming technologies that Robotnik could use to kill all life on Mobius by teraforming the environment so that there is no longer enough oxygen for example... and once everyone is dead except him and those loyal to him or those who have been roboticized, he could change it back or into anything else he wanted. Samuel would definitely have to either reclaim the ship by any means possible or destroy it if he can't reclaim it.
And if your wondering Samuel would never work with a Space pirates (over the Freedom Fighters) as he has no more trust for them than he does for Robotnik.
Timothius:
**** VALIN
Valin gets provoked to violence
That would be scary.... Hulk... I mean Valin Smash!