NPC Missions

EDIT: You didn't mean storyline missions, did you?

If you did...
Add an npcship entry in npcships.ini in the MISSIONS directory.

[NPCShipArch]
nickname = MSN_Gunboat
loadout = rh_gunboat
level = d1, d2, d3, d4, d5, d6, d7, d8, d9, d10, d11, d12, d13, d14, d15, d16, d17, d19
ship_archetype = rh_gunboat
pilot = gunboat_default
state_graph = GUNBOAT
npc_class = lawful, class_fighter

This is NOT perfect and may not even work, and also it will spawn along with fighters when you're not doing random missions.

Next, add a line to the end of the faction you want in factionprops.ini in the MISSIONS directory:

npc_ship = MSN_Gunboat

I thought this out from the back of my head, so like I said, it's NOT perfect.

If you DID mean storyline missions, then here's my LONG reply that I am not willing to delete:
Hi, storyline missions are my favorite part of modding, so i'll give you some code...

In npcships.ini, put in:

[NPCShipArch]
nickname = MSN_Gunboat
loadout = rh_gunboat
level = d12
ship_archetype = rh_gunboat
pilot = gunboat_default
state_graph = GUNBOAT
npc_class = lawful, class_gunboat

You can see that i'm using the Rheinland gunboat as a template. You can change this to whatever you like (br_gunboat being Bretonia Gunboat, ku_gunboat being Kusari Gunboat)

If you want a Cruiser:

[NPCShipArch]
nickname = MSN_Cruiser
loadout = li_n_li_cruiser
level = d18
ship_archetype = li_cruiser
pilot = cruiser_default
state_graph = CRUISER
npc_class = lawful, CRUISER

Change li_cruiser to whichever cruiser is appropriate (rh_cruiser, ku_destroyer, br_destroyer)

And finally a battleship:

[NPCShipArch]
nickname = MSN_Battleship
loadout = li_n_li_dreadnought
level = d22
ship_archetype = li_dreadnought
pilot = cruiser_default
state_graph = CRUISER
npc_class = lawful, battleship

Again, change li_dreadnought to whatever you like (rh_battleship, ku_battleship, br_battleship)

(Put only what ships you need in npcships.ini)

Now for the main mission code.
I'll give you a template Obj List, NPCs, formation, and ships:

[NPC]
nickname = m_gunboat
affiliation = rh_n_grp
npc_ship_arch = MSN_Gunboat
individual_name = 216511
voice = pilot_f_mil_m02
space_costume = rh_captain_head, rh_male_elite_body, prop_neuralnet_D

[NPC]
nickname = m_cruiser
affiliation = li_n_grp
npc_ship_arch = MSN_Cruiser
individual_name = 216303
voice = pilot_f_mil_m02
space_costume = li_captain_head, li_male_elite_body, prop_neuralnet_D

[NPC]
nickname = m_battleship
affiliation = li_n_grp
npc_ship_arch = MSN_Battleship
individual_name = 216300
voice = pilot_f_mil_m02
space_costume = li_captain_head, li_male_elite_body, prop_neuralnet_D

Theres the NPCs declared... now onto the msnship declarations.

[MsnShip]
nickname = gunboat_1
NPC = m_gunboat
position = 10000, 5, 20000 ;If you plan on using a formation, delete this line.
;orientation = 1, 0, 1, 0 ;Uncomment this line if you want to use orientations
label = capships

[MsnShip]
nickname = cruiser_1
NPC = m_cruiser
position = 10100, 5, 20000 ;If you plan on using a formation, delete this line.
;orientation = 1, 0, 1, 0 ;Uncomment this line if you want to use orientations
label = capships

[MsnShip]
nickname = battleship_1
NPC = m_battleship
position = 10300, 5, 20000 ;If you plan on using a formation, delete this line.
;orientation = 1, 0, 1, 0 ;Uncomment this line if you want to use orientations
label = capships

Here is a template formation (don't use this if you're only using one or so ship):

[MsnFormation]
nickname = capship_formation
position = 10100, 5, 20000
orientation = 1, 0, 1, 0
formation = cruiser_wall ;If you're using gunboats only use gunboat_rh_n, gunboat_ku_n, or gunboat_br_n depending on the gunboat used
ship = battleship_1
ship = cruiser_1
ship = gunboat_1
;ship = escort1
;ship = escort2 ;Use these if you have other ships in the formation
;ship = escort3

Now an objlist:

[ObjList]
nickname = fly_to_p1
GotoShip = goto, Player, 800, true ;Swap out 'Player' for the ship or solar you want the formation or ships to fly to.

Now some template triggers I too kindly cooked up for you, simply fire off 'spawn_capships' to spawn the formation. And feel free to change any labels where needed, or delete any lines where needed.

[Trigger]
nickname = spawn_capships
system = Li01 ;This line assumes you are in the New York system. For all other triggers with this line, simply change Li01 to the system you are in.
Cnd_Destroyed = badboys, 4, ALL_IGNORE_LANDING
Act_SpawnFormation = capship_formation ; Or SpawnShip = (ship)
Act_GiveObjList = battleship_1, fly_to_p1
Act_SetVibeLblToShip = capships, Player, REP_FRIEND_THRESHOLD
Act_SetVibeShipToLbl = Player, capships, REP_FRIEND_THRESHOLD
Act_ActTrig = nearing_p1

[Trigger]
nickname = nearing_p1
system = Li01
Cnd_DistShip = inside, battleship_1, Player, 1200
Act_SetVibeLbl = capships, badboys, REP_HOSTILE_MAXIMUM
Act_SetVibeLbl = badboys, capships, REP_HOSTILE_MAXIMUM
Act_SendComm = battleship_1, Player, rms_friendlyarrival_01- ; Change the number to 02 or 03 for different results.
Act_ActTrig = rms_comm_done

[Trigger]
nickname = rms_comm_done
system = Li01
Cnd_CommComplete = rms_friendlyarrival_01- ; this needs to be the same as the comm you fired off in the last trigger.
...etc

This code may not apply to the mission you're cooking up, so i'm sure you'll need to change it to what you had in mind.