You can spawn the unit you want dead with the player, and the rest of his squad away from the player, in a middle of an overwhelming amount of ennemies. They'll blow the rest of the squad, while the player kill the single unit. It will appear as there was only 1 unit. However, most space squad have only 1 ship if the player is alone. If you don't choose frigates/fighters. They will appear as a full squad on the foundry map during creation. More of them will only come if the player play the map with others, but you can specify the map is made to be played alone.
If you still want 1unit only, even for groups, you'll have to deal with several issues. First, make sure the hidden fight is won by the player's NPC allies, not his/her ennemies. Also, you'll have to hid them, and put walls so they won't escape their fate.
On a ground map it's not really difficult, on a space map, well I don't know...
I see what you're talking about, i want want my unit to be able to disappear and appear. But a squad of enemies wont do such a thing
You can set the name of any objective to whatever you want. Set up a reach marker around your cube and set the diameter to slightly less than the 10 km. In your story assign the objective to 'reach marker' and rename it to 'destroy borg cube' although the objective will complete before it is actually destroyed your player will be in combat and nothing progresses under red alert.
As for the disappear then appear. You can only make anything appear then disappear. You will have to work your story around that limitation.