Roxann Dawson (B'Elanna Torres) went into labor during the production of this episode. That is why B'Elanna is seen in Engineering towards the beginning of the show, but is strangely absent when Captain Janeway briefs the senior officers during the special meeting about Omega.
Janeway's log entries are encrypted throughout this episode. In one of her log entries, Janeway makes mention of Star Trek II: The Wrath of Khan (1982)'s Dr. Carol Marcus and the Genesis Device. In fact, the Genesis Device was originally called an "Omega" device in early story treatments of the film.
This is the only time Janeway, or any other captain, is established as officially rescinding the Prime Directive.
Harry Kim is shown playing kal-toh, after Tuvok offered to teach him the game during Alter Ego (1997).