I took a quick look of the mission in Notepad, and:
1) The cruisers do not have a departure cue,
$Name: Bane ;! Object #45
$Class: SC Cain
$Team: Hostile
$Location: -6139.924805, -0.000154, -18636.003906
$Orientation:
0.997925, 0.000000, -0.064384,
-0.000590, 0.999958, -0.009150,
0.064381, 0.009169, 0.997883
$IFF: IFF 1
$AI Behavior: None
$AI Goals: ( goals ( ai-waypoints "Waypoint path 7" 50 ) )
$Cargo 1: XSTR("Nothing", -1)
+Initial Velocity: 100
+Initial Hull: 100
+Initial Shields: 100
+Subsystem: Pilot
+Subsystem: turret01
+Subsystem: turret02
+Subsystem: turret03
+Subsystem: turret04
+Subsystem: turret05
+Subsystem: turret06
+Subsystem: turret07
+Subsystem: turret08
+Subsystem: turret09
$Arrival Location: Hyperspace
$Arrival Cue: ( is-destroyed-delay 15 "Thanatos" )
$Departure Location: Hyperspace
$Departure Cue: ( false )
$Determination: 10
+Flags: ( "no-shields" )+Respawn priority: 0
$Name: Melchom ;! Object #51
$Class: SC Cain
$Team: Hostile
$Location: -6221.718750, 0.000082, -17867.998047
$Orientation:
0.996724, 0.000000, -0.080878,
-0.000795, 0.999952, -0.009793,
0.080874, 0.009826, 0.996676
$IFF: IFF 1
$AI Behavior: None
$AI Goals: ( goals ( ai-waypoints "Waypoint path 8" 50 ) )
$Cargo 1: XSTR("Nothing", -1)
+Initial Velocity: 100
+Initial Hull: 100
+Initial Shields: 100
+Subsystem: Pilot
+Subsystem: turret01
+Subsystem: turret02
+Subsystem: turret03
+Subsystem: turret04
+Subsystem: turret05
+Subsystem: turret06
+Subsystem: turret07
+Subsystem: turret08
+Subsystem: turret09
$Arrival Location: Hyperspace
$Arrival Cue: ( is-destroyed-delay 15 "Thanatos" )
$Departure Location: Hyperspace
$Departure Cue: ( false )
$Determination: 10
+Flags: ( "no-shields" )+Respawn priority: 0
2) The supernova only happens if Libra wing has been in the mission, and Libra wing warps in when either the Bane or the Melchom are destroyed.
$Name: Libra
$Waves: 2
$Wave Threshold: 0
$Special Ship: 0 ;! Libra 1
$Arrival Location: Hyperspace
$Arrival Cue: ( or
( is-destroyed-delay 5 "Bane" )
( is-destroyed-delay 5 "Melchom" )
)