Okay, so let's ponder for a moment. The characters seem very well equipped to handle a lot of things. They also seem to have enough smarts to either deduce (INT) or remember( EDU) well, giving them positive modifiers for mental skills. If you all have been playing for several years then you probably are running well and everyone is having fun.
Have you tried a multi-level root cause campaign? Let's say Professor Sorokos, one of the characters favorite instructors back at Miskatonic U, dies unexpectedly. The character is asked to attend because of their relationship, and the character is in the will. As an aside, the character is asked to carry a few things of sentimental value to another couple professors, in different directions but not really too far out of the character's way.
Sadly, that professor recently passed away. So did the other one. Circumstances seem almost normal, but coincidence is too strong. So, the characters can investigate. And they probably should, since one of their relatives/close friends may also be on the "scheduled to have an accident" list.
Start with a mystery where the characters don't know exactly where to look, but they do need to make decisions that put other things at risk.
Now, come in from another direction. A few reports have been coming in of some pirate raids by a ship 2-4 times larger than the PC's ship. Of note in the reports is that whoever is flying the pirate ship can just about make it turn on a dime and dance a jig; they are that good. The clues for the deaths may be in the same area as the pirate activity, but maybe not.
Now add the "your'e an outsider" factor. If you've ever moved or traveled a lot you know the feeling. You pretty much have to ask for everything specifically as you don't have any relationships in that area. Further, organizations don't treat you the same until you've been there a dozen or more years. Neither of the characters is a noble, but maybe they want to be? Especially since the folks who seem to be dieing were moving up in the social ladder. Is there some jealous blue blood who hates the middle class?
Next angle, there's an outbreak of some long eradicated disease in the Goram system. By the time the characters hear about it further the disease has started to spread, and there is some overlap between the pirate activity and the disease.
Remember the military characters crazy Aunt May? The one that ran off and joined a cult at age 16 and is now in her 50's? She's a popular entertainment vid mystic charlatan. Or she was, until some of her more dire and obscure predictions started coming true. Add the possibility of hokey religions.
Before this gets further, take some of the potential events and tie them to the PC's backgrounds. If they've been travelling for a decade or so then they probably have friends and enemies in abundance. Connect the PC's history to the impending future.
So far there's a challenge or two (someone with higher skills), a mystery or three (are any of these connencted?), a wide enough playing field that the characters can't be everywhere at the same time, a few social organizations (nobles, schools, corporations, pirates) that won't necessarily talk openly, and a time crunch (the deaths are spreading).
There is a root cause, maybe more than one. But put a few layers between the noticed events and the "root of all evil". Maybe the evil isn't that bad at all? Maybe it's a good thing just off kilter? There will be bad guys to shoot, but the final solution isn't resolved by combat. There will be space to explore but the risks are greater unless the characters are using a larger ship, which means other people, and other risks, are involved. Some of the risked is personal; friends and family of the characters. Making one choice may preclude making other choices.
Time is short, what do you do?
#######
Scout 6C9EC8 Age 36
Combat: Pistol-0, SMG-1, Combat Rifleman -1, Brawling-0, Handgun -0, Shotgun -0, Short Blades -0
Low Social: Streetwise -0, Gambling -0, Carousing -0, Bribery -0
Ship: Ship Tactics -0, Mechanic -0, Air/Raft -0, Computer -0, Communications -0, Electronics -0, Gravitics -0, Vacc-Suit -1, 0g Envrion/Combat -0, Pilot-2, Survey-2, Engineering -1, Gunnery -1, Navigation -1, Robotics -1
People: Liaison -0, Linguistics -0, Admin -0
Wilderness: Survival -1, Hunting-0, Recon-0
Misc: Medical-0, JoT -1, Psionics -1
Military 7A8EDA Age 33 (?)
Low Social: Streetwise-0
Wilderness: Prospecting-0, , Survival-1, Recon-1
People: Liaison-1, Instruction-1, Psychology-0, Lots of languages at high level of fluency.
Combat: 0g Combat-2, 0g Weapons-2, Combat Rifleman-2, Laser Weapons-1, Grenade Launcher-1, Handgun-0, SMG-0, Tactics-1, Demolitions-1, Short Blade-0, Melee Combat-1, Large Blade-1
Ship: Navigation-0, NV Commutations-1, Pilot-1, Ships Boat-2, Computer-0, Eletronics-0, Grav Vehicle-0, Vacc Suit-2, Gunnery-1
Misc: Psionics-1, Medical-0