Here's an example file mod. I used when designing "ISC Invasion" campain.
You edit the ISC-Fed.gf file in the "assets/script/campaign" folder:
Name="ISC Invasion"
Description="Play as the Federation against the ISC and their war of pacification."
EarlyMapName="ISCInvasion.mvm"
MidMapName="ISCInvasion.mvm"
LateMapName="ISCInvasion.mvm"
DifficultyLevel=1
Era=0
TriggerMission="Uni_1Peace"
TriggerPrestige=800
[Missions]
0="Kar_1Scout.scr"
1="Kar_2HoldingAction.scr"
2="Kar_3Ambushee.scr"
3="Kar_4Ambusher.scr"
4="Kar_5FleetAction.scr"
5="Kar_6Patrol.scr"
6="Kar_7BaseAssault.scr"
7="Kar_8ShipAssault.scr"
8="Kar_9PlanetaryAssault.scr"
9="Kar_10Patrol.scr"
10="Kar_11ConvoyRaid.scr"
11="Kar_12ConvoyEscort.scr"
12="Kar_13Monster.scr"
13="Kar_14Enigma.scr"
14="Kar_15BaseDefense.scr"
15="Kar_16ShipDefense.scr"
16="Kar_17Patrol.scr"
17="Uni_1Peace.scr"
18="Uni_2Promises.scr"
19="Uni_3IronCage.scr"
20="Uni_4Resolve.scr"
21="Uni_5Accuse.scr"
22="Uni_6Immunity.scr"
23="Uni_7BattleGrave.scr"
24="Uni_8Hammer.scr"
25="Uni_9A1Tyr.scr"
26="Uni_9C1Welcome.scr"
27="Uni_10Criminals.scr"
28="Uni_X3M1ATemple.scr"
29="Uni_X4M1AThief.scr"
30="Uni_X4M2ACuckoo.scr"
31="Uni_X4M3ADoors.scr"
32="Uni_X1M1ASmuggler.scr"
33="Uni_X1M1FInsurrection.scr"
34="Uni_X1M2Trial.scr"
35="Uni_X1M3Poison.scr"
36="Uni_X5M1AMoon.scr"
37="Uni_X5M1FPyre.scr"
38="Uni_X5M2Sake.scr"
39="Kar_18HomeworldAssault.scr"
40="Kar_StarbaseConstruction.scr"
41="Kar_19Scan.scr"
[Races]
0=0
Basically the TriggerMission is set to go off when you reach 800 pp which will play the in-box campaign. However, the maps and the other missions are customized.
GL and HF.