The subspace missiles are called by a tag missile which is created using 'weapon create'. That tag weapon has been assigned a parent 'Ship', which is unkillable and persistant throughout the mission.
Here is the table for that ship:
$Name: Empty
$Short name: Ptracker ;;just a crutch to fight FRED with
$Species: Terran
$POF file: Empty.pof
;Detail distance is Irrelevant
$Density: 1
$Damp: 0.2
$Rotdamp: 0.2
$Max Velocity: 0.0, 0.0, 0.2
$Rotation time: 20.0, 20.0, 20.0
$Rear Velocity: 0.0
$Forward accel: 0.0
$Forward decel: 0.0
$Slide accel: 0.0
$Slide decel: 0.0
$Expl inner rad: 0.0
$Expl outer rad: 0.0
$Expl damage: 0.0
$Expl blast: 0.0
$Expl Propagates: NO ;; If set to Yes, then when the ship dies, the explosion propagates through it.
$Shockwave Speed: 0.0 ;; speed shockwave expands at, 0 means no shockwave
$Default PBanks: ()
$Default SBanks: ()
$SBank Capacity: ()
$Shields: 0
$Power Output: 0.0
$Max Oclk Speed: 0.0
$Max Weapon Eng: 0.0
$Hitpoints: 100
$Armor Type: Normalspace
$Flags: ("no_collide" "cruiser") ;;cruiser to make AI know what it's attacking in the Sapphire mission
$AI Class: Grunt
$Afterburner: NO
$Countermeasures: 0
$Scan time: 2000
$Closeup_pos: 0.0, 1.0, -28
$Closeup_zoom: 0.5