What I mean is this. My mission is for Fed faction, but takes place mostly in Klingon space. I'd like to have the player meet a Klingon character who joins him to fight a common enemy. Is this possible?

It sure is! What you do is you place a Federation NPC group of your choice on the map. Then zoom in till you see the individual red dots that represent each ship. Click on each of these dots and you will see a button at the bottom of the screen that says Costume, click it, and you will get a pop up menu where you can select any ship in the game, as well as any custom ship costume you might make.

Alternatively, you can also select each individual ship by looking at the left-side menu and clicking on the little grey triangle next to the name of the NPC group, it will expand the group to show you each individual ship.

The caveat is the group will still fight like Federation ships, even if they look like something else. They will use Federation weapons and Federation skills. Right now we don't have the option to change that.

So can I use this same procedure on a ground npc group, to have a Klingon fighting alongside the Federation character?

Yup, just change the actor costumes

Awesome, Thanks fellas

Oh I forgot... Can I delete some of the "actors", so there is just the one character?

Unfortunately not - Also note that this group costumed as Klingon will still fight as Federation.

If it's an outdoor map, your best option would be to have the other actors spawn far away where the player can't see them, and very high in the sky. So, when the mob spawns, all the unwanted actors will spawn and just fall to their deaths, unseen to the player.

If you're making a "custom indoor" map (i.e. an original building interior built with Foundry assets on a technically outdoor map), then you can just have the unwanted players spawn at a ridiculously high altitude, and then they'll just fall and die on top of the roof.

As for a Foundry-supplied indoor map, your best bet would to just have them, again, spawn high, and maybe at the "unused" portions of the map.