The Gamma Quadrant is home to the Changelings, or Founders. The majority of it is ruled by the Dominion.

An ion storm causes a transporter malfunction, and the landing team instead materialize aboard an unfamiliar Enterprise. Their alternate universe counterparts simultaneously materialise on the Enterprise in the Federation universe, and are thrown in the brig by Mr Spock who immediately recognizes the changed personalities of the barbarian landing party.

Denise Crosby was originally cast to play Counselor Troi, and Marina Sirtis was cast as security chief Lt. Macha Hernandez, but they switched roles during rehearsals and the security chief's name was changed to Lt. Natasha Yar.

Dr. McCoy is treating an injured Lt. Hikaru Sulu when the Enterprise is rocked by a distortion and McCoy accidentally injects himself with an overdose of cordrazine which makes him temporarily insane.

Frustrated with the lack of character development for Dr. Crusher, Gates McFadden clashed with producers which led to her release after the first season. In Season 2, Dr. Crusher was replaced by Dr. Kate Pulaski, played by Diana Muldaur. However, producer Rick Berman personally phoned McFadden to convince her to return for Season 3.

As a running gag, bathrooms never appear on Enterprise schematics. This joke is referenced in Star Trek: First Contact when Zefram Cochrane asks Geordi, "Don't you people from the 24th Century ever pee?"

Worf's prosthetic forehead changed in season 2 because the original was stolen.

Kirk is nearly assassinated by Chekov and his henchmen, one of whom betrays Chekov and saves Kirk's life. Later in the same episode, Sulu attempts to assassinate Kirk as well.

After being transported to the alternate Enterprise, Kirk finds the beautiful Lieutenant Marlena Moreau, who refers to herself as the "Captain's Woman", stretched out on his bed.

Fek'lhr was a monstrous, feral Klingon who was believed to guard the gates of Gre'thor.