I have begun work on a storyline involving the colony of Borg that Janeway left on a planet on Voyager: Unity.
After checking the EULA as long as I do not use the likenesses of any of the shows characters I can use this as a story correct? and if so how much can I use? I plan to tie it in to a "supposed" invasion of ESD. I want to awnser the question of "WHere are they now?" so to speak.
You have it correct, as long as you use no actor's likenesses, you may proceed.
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It is also permissible to show log entries or "audio recordings" from a canon character, but the safest way to do this and not run afoul of the EULA is to make the costume for that dialogue a console, not anything even close to a person's likeness.