There may come times when you may wish your characters to interact with starship combat using either StarFleet Battles or the Fleet Combat System. If you do, then this section is for you.
If you are using one of the alternate starship combat systems, then consult the various notes there for integration with that system.
Proper rules for this in the Prime Directive rulebook, section [8] page 164.
However, not all characters may conform to the standard templates given, and thus it may be necessary to know where characters are in case they are in a section that gets hit.
Movement through a large ship should be done via boarding party movement (one section per SFB turn), and at the end of each turn the character should select which box on the SSD they are in, or if just passing through, then a hull box will be the selected box (if one is present). If this box is then damaged or destroyed, the character should take 3d6 crushing damage. This represents the various section of the ship being blown apart - just like in the series, with girders falling down, people being thrown around the room and falling over consoles and the like.
Obviously you will have to use common sense as to the placement of the characters when in a combat situation. Bridge crew (pilots, astrogators, sensor operators, the Captain) will all be on the bridge, although the Captain may move off. Warriors will be around the flight decks. Medics will be either in the life station or out tending the wounded. All crew have a part to play, and there are strict disciplinary measures for those who abandon their posts.
If in a smaller ship (such as a fighter or shuttle), then there really is not anywhere for a person to run to, and similarly nowhere for an explosion to vent to. Thus if the station where the character is in is hit, then the damage is 6d6 crushing.
Gamesmasters may allow vacc suit skill rolls, DX success rolls, or simply luck rolls for characters to escape from a doomed vessel.
Due to the scales of the games involved, there is not actually a lot that can be combined between the two systems of GURPS and the FCS.
The only skills that will have much bearing at this scale are Strategy and Piloting (Fighter craft).
At the beginning of each turn, the commanders of each fleet should make a strategy contest of skills roll. Whomever wins has initiative for that turn.
This skill only comes into play if the character is piloting a fighter in a flight that has just been destroyed. If this is the case, then the character should make a piloting skill roll.
On a critical failure, the character and their craft were destroyed.
on a failure, the character is okay, but their craft is severely damaged. Whomever wins the overall fight will be able to retrieve the character, but the fighter itself will not be able to leave the fight under its own power.
On a success, the fighter is damaged, but the character is fine. The craft will be able to leave the battle under its own power and even be able to jump away.
On a critical success, the craft and the pilot are fine, no damage having been sustained.
If a ship (save a fighter or shuttle) is destroyed that is carrying characters, then the gamesmaster may allow a success roll vs. DX to see if the character got to a rescue pod or shuttle in time.