I am trying to create a mission with action similar to the fleet battles in the missions "Preemptive Strike", "Diplomatic Orders", and "The New Link" I have set the ships, and the enenmy groups. How do I get them to start going at it, with support from the player?

Also, I would like to eventually edit the ships in the map so that I can have one of the ships be a Dreadnaught.

Put a romulan NPC group next to a Klingon NPC group. Works with all different NPC group factions. Then go into the group on the Placed items list of you map and click on the npc Group. You can place different costumes on all the different actors in the group. Space NPC groups do level. So if there is more than one player playing your mission at a time the NPC group will scale.

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Do they have to be NPC groups? I can't use NPC contacts? My example is a group of 4 Federation Saber class ships beside a group of Terran Starfleet ships.

contacts usually just sit there and take abuse, rather than actively participate. besides you are limited in the number of contacts you can place on a map, so its more economical to use NPC groups