I'm probably not the only person who has ever wanted to make a plugin similar to the Wing Commander games. In such a plugin, you would begin and end each mission launching from a mothership of some sort. However, unless the "mothership" is really a spöb (and thus boring and not a ship), this can't be done.
UNTIL NOW! (dramatic music)
Ladies and gentlemen, upon reflection I have concocted the following solution to this scenario. I don't personally have the time to make any plugs that use this system, but the possibilites are many. A TC that uses this would be interesting, but what about in the standard game? A plugin that adds military service as a fighter pilot in the Federation or Auroran Empire would be interesting and certainly novel. If you do decide to use this system, mention my name somewhere in the credits, please.
The trick is to do the following:
Once the goals of a mission has been completed, use the Axxx set expression to abort the mission and the Sxxx to begin a secondary, hidden mission with the same name. This mission will have the special ship goal to be board the mothership after hailing it. On the completion of this mission's ship goal, use the Mxxx set expression to move the player to a special system, which has a (preferably animated) spöb with the graphics of the base ship. Refueling, rearming, and selecting a new mission would take place on the "mothership" spob. Once a new mission is accepted, use the Mxxx set expression to move the player to the site of the new mission.
This could be combined with making "systems" that include a number of s˙st resosurces and are connected by wormholes. Only ships with a hyperdrive outfit can use the wormholes, so intrasystem travel is possible but not intersystem travel.
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To quote a pillar of American society: D'OH!