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 scoutship 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")