Federation ships (or Klingon for klingon missions), as well as the ground mobs for respective factions, are already allied with you and will attack mobs that are your enemies, by mobs, i mean the npcs in the 'npc group' list you pick enemies from, not 'npc contacts'.
Just place the friendly mob near the enemy one. As long as they are in range of each other, they will attack each other.
However if you're talking about when you're using friendly contacts who will fight, but also allow you to interact with or talk to afterward, then it gets abit more complicated. Contacts, unlike encounter mobs, will not fight, but you can still use the npc mobs instead of npc contacts for this.
Only in your case, you'd do it in space instead of on a ground map (note that npc mobs return to their original location after fighting, so this still works, as long as they didnt die), and there are now 'invisible objects' that we can use in lieu of Kirkfat's volcanic flower example. In a nut-shell, you have the player interact with the invisible object which is in the same location as the friendly mob, so it makes it seem like they're interacting with the friendly mob.
I created a True Way Battleship, and a NPC Cardassian Ship (It's green on the map, friendly, and I am able to talk to them).
So, I want them to fight each other while I come to the NPC Friendly's rescue. But they don't. They just sit there idle until I enter range, then the True Way ship attacks me.
So, why aren't they attacking each other? It is registering as "Alien Cruiser" on the map when I play it.
Ok in this case i need to clarify some things. All 'npc contacts' no matter what they are, are green and friendly. However, they also dont fight at all.
'Npc groups's, such as the true way battleship you created, are able to fight. Furthermore, npc groups in that list matching your faction (federation for fed, klingon for klingon) are allied with you despite the fact that they also appear red on your editor map. You can preview this to check.
In your case, you would place, say, a federation battleship from the 'npc groups' list. There is a 'costume' selector in the 'general' tab for each actor in the npc group u just placed. You'll use that to recostume the ship as the friendly npc cardassian ship. When it fights, it will use weapons and powers as if its the fed battleship, but thats unavoidable.
Did this solve your problem?
EDIT: Btw, all space contacts default to 'alien cruiser' if you dont name them, also under the 'general tab'.
EDIT2: I really need to get to sleep. If you do need more help, i hope someone else can pop in here. Or you can go through the tutorials at StarbaseUGC.com or visit the chat there, there may be people online willing to help. And i'll of course look here again later...
The NPC contacts aren't actually active for combat, only the NPC groups will fight. And the only NPC groups that are allied with you are the Federation ships. So, what you need to do is reskin a Federation group to look like Cardassians. It will still actually be a Federation ship, and it will have that weapons load out, but it will look like a Cardassian ship (this actually works really well with Cardassians since they use phasers just like the Federation. It's kind of weird with other ships because it will be obvious they are using the wrong energy weapons.)
What you need to do is remove the Cardassian NPC and put in a Federation Cruiser group instead (not Mirror Federation!), or maybe a Federation Science group if you're using Galors. Then expand the group and select each actor.
Under the actors there will be an entry called Costume. Hit that, then select a Cardassian Keldon/Galor/etc. Under the Contact entry, you also need to set the name to be whatever ship you selected, otherwise it will still list as the default (ie: Federation Cruiser) even though it looks like a Cardassian.
Now, as far as the ship talking to you when combat is over, you can do it one of several ways:
1) First of all, you can make it a mission objective in your storyline to help the vessel. Which really means you set an objective that triggers off of killing the attacking group. Then you'd put a dialogue as your next storyline entry, which would cause it to pop up automatically.
2) If you want the player to actually have to interact with the vessel, then you can do the same as above, but place an invisible object or small asteroid in the same place as the friendly group. Select that object and choose States. Then select objective complete and then hit the entry area underneath and select the objective to kill the attacking group. Now add another objective to your storyline and select the invisible object. Change the interact text to be "Hail Cardassian Ship". Then place your dialogue as the next storyline entry after that.
You can also do roughly the same thing but use Component Complete triggers instead (component complete means that the individual item is interacted with, the specific enemy groups are destroyed, etc, even if they're not part of your storyline objectives). In that case you'd need to select the State tab on the dialogue and interact object and set them to not appear until the proper conditions have been met. With this method you can essentially put in secondary objectives outside of the main story. In your case since this is part of your main storyline, using that method would probably be easiest.
There is one possible flaw in this setup. That is if the Cardassian NPC ships (reskinned Federation ships) are killed, you'll still be able to hail them afterward. To avoid that, you could place an NPC Cardassian Contact to spawn after the battle is complete. You could even select to have it be damaged using either the FX Damaged or the FX Leaking under Behavior>Idle A animations. To do that you'd place the NPC Cardassian and then select States and select either Objective Complete and select the Objective that triggers off of killing the enemy group, or select Component Complete and simply select the enemy group as the trigger. However, by doing that you'll spawn an extra vessel which could look weird if the other ship(s) survive. So it's kind of a "pick your poison" situation.
I did not get it to work yet. I created a True Way Squadron - the enemy.
Then I create a federation squardon as you suggested. If I do nothing else and run the map, it works. However, there are no "Cardassian" ships in the costume slot (It's labeled encounter, not costume, but it does change the appearance). So, if I select True Way squadron as a costume, they are both allied again.
I think my problem is that there is no "Cardassian" faction, and that I am trying to use True Way for both. This is a little frustrating.
EDIT - just read the above post and will try the individual costume slots! Thanks!