The series focuses on the Mayor of New York City, Randall Winston (Barry Bostwick), and his staff as they run the city — although the main person in charge is Deputy Mayor Mike Flaherty (Michael J. Fox). Mike is excellent at his job, dealing with spin and lies, but not so good with his personal life, which he often neglects. Other members of staff at City Hall include press secretary Paul Lassiter (Richard Kind), the office cheapskate, suck-up, and noted coward, who has a habit of being a loudmouth and is often kept in the dark about things; assistant deputy mayor Stuart Bondek (Alan Ruck), who loves the ladies and is often very sexist; head of minority affairs Carter Heywood (Michael Boatman), who is a gay black man who owns a suicidal dog named Rags. Despite their overwhelming personal differences, Stuart and Carter actually become roommates and the best of friends; speech writer James Hobert (Alexander Chaplin), who is easily led and quite naive; Mike's secretary Janelle Cooper (Victoria Dillard); and his assistant Nikki Faber (Connie Britton). Janelle later became the mayor's secretary and Stacy Paterno (Jennifer Esposito) joined the show as Mike's. Each of them has to help run City Hall, improving the Mayor's image and cover for his frequent gaffes, while sorting out their personal lives.

At the start of the series, Mike is dating reporter Ashley Schaffer (Carla Gugino). In early promos for the series, this relationship is shown to be the main premise of the show. However, just a few episodes into the series, Gugino decided to leave. Rumours indicated that Fox's wife Tracy Pollan was not happy with the love scenes between Fox and Gugino's characters (some say that their chemistry was "too good")[citation needed], and indeed one episode ("A Star Is Born") was re-edited for syndication, with all scenes featuring Ashley removed and replaced by other scenes.

The bond between Carter and Stuart became something of a running gag during the series. The two ended up becoming so close that their friendship was mocked by others and their arguments sounded so much like husband and wife that a whole episode was dedicated to the notion that the two argued like a married couple. The two ended up meeting an older duo of best friends (one black and one white) that were virtual twins of Carter and Stuart in terms of personality. When it was discovered that the two older versions had become a couple it ended up scaring Stuart quite a bit. For his part, Stuart tends to be very possessive of his time with Carter, going so far as to be genuinely jealous when Carter spends more and more time with Caitlin. In spite of all the jokes and innuendos regarding the two, they prove to be best friends willing to do anything for both their friends and each other. Fans of the show have often compared them to the The Odd Couple, with Stuart being the sloppy, hedonistic Oscar to Carter's uptight, fussy Felix

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