A mother ship was a large spacecraft on which a smaller ship was carried, maintained, and launched.
In 2266, after the USS Enterprise broke free of the tractor beam emitted by a pilot vessel, this vessel sent a weak distress call to its mother ship Fesarius. Communications officer Nyota Uhura doubted that the mother ship could have heard the call. (TOS: "The Corbomite Maneuver")
In 2366, after the Enterprise rescued the Romulan officer Patahk from Galorndon Core, after his scout ship Pi crash landed on the planet, Commander Riker asked him if there was a mother ship that should be advised of his condition. (TNG: "The Enemy")
In 2369, after Pup made its appearance in the Alpha Quadrant, Commander Benjamin Sisko asked Jadzia Dax if it was a probe. She responded that it might be; however, she wasn't finding signals that would indicate the alien spacecraft was maintaining contact with a mother ship. (DS9: "The Forsaken")
In 2376, Dala, posing as Captain Kathryn Janeway, asked Zar, posing as Commander Chakotay, to place a master situation display of the USS Voyager on a viewscreen for Varn to see. (VOY: "Live Fast and Prosper")