Workaholic Mike Flaherty is the Deputy Mayor of New York City, serving as Mayor Randall Winston's key strategist and much-needed handler. Mike runs the city with the help of his oddball staff: an anxious and insecure press secretary; a sexist, boorish chief of staff; an impeccably groomed gay activist running minority affairs; a sharp and efficient, man-crazy accountant; and an idealistic young speechwriter. Like Mike, they are all professionally capable but personally challenged.
Mike shows up at Caitlin's to announce that he's met someone. Meanwhile, the mayor is dating a judge who's not yet divorced. Charlie suggests that the mayor break it off, but after getting some advice from Mike, he decides to let the mayor do what makes him happy. Charlie impresses Caitlin but Mike interrupts again to announce his engagement.
The mayor has a tree cut down to impress his new girlfriend. Unfortunately, it was a tree planted by George Washington in 1796. Meanwhile, Charlie has a one-night stand, who turns out to be a rival mayoral candidate's campaign manager. Mike helps out with crisis control. Charlie and Caitlin decide to be friends for the time being, while Mike announces his return to City Hall.
Mike calls off his engagement with Allison and increases his presence in the office, making Charlie feel threatened. However, Charlie talks him into staying with Allison and marrying her--in City Hall. Meanwhile, Caitlin helps the mayor dress like a woman for a charity event.
The mayor's approval ratings are going down, thanks to his relationship with the not-yet-divorced Judge Simmons. Charlie convinces the mayor to seek quiet time with Claire at a friend's house--only he didn't anticipate the mayor showing up at his. Paul hires a publicist to improve his image. After going to a friend's baby shower, Caitlin becomes obsessed with having a baby. Carter lets her watch Rags for a day, but he swallows Charlie's pager. Caitlin decides not to have a child, but apparently, Carter does.
Carter's friend Michelle visits and begins dating Stuart. However, Carter has just asked her to be his child's surrogate mother. Meanwhile, Charlie and Caitlin struggle over what to do with incriminating photos of the mayor's opponent.
The mayor hires a political strategist to act as his campaign consultant. The consultant, Robin, is a bit of a psychic, predicting that a date of Charlie's will result in disaster, so Caitlin rushes to save him. As Stuart becomes more involved with Michelle, she tries to determine whether she is pregnant with Carter's artificially inseminated child yet. Stuart realizes that he may be the father after revealing that he forgot protection one night. However, Michelle discovers that she's not pregnant.
The mayor prepares to debate his opponent, while Charlie and Jennifer, his opponent's campaign manager have been dating for 3 weeks. The mayor wants Charlie to dump her, but he doesn't. When the mayor visits Charlie in the middle of the night to share something that may be damaging to his campaign, Jennifer may have overheard it. Meanwhile, Paul and Robin become involved; Paul thinks it's a relationship, while Robin thinks it's a fling.
Charlie discovers that Jennifer's ex is a woman. He becomes jealous when watching her be affectionate with Caitlin, something Caitlin dismisses until Jennifer kisses her on the lips. Claudia and Paul's divorce settlement may be affected by the mayor's bickering with Judge Claire.
Caitlin's mother Jane comes to visit when Caitlin tells her she finally has a boyfriend. In a panic, Caitlin enlists Charlie to play the part, and Charlie gets stuck having to attend a family wedding to help her. Meanwhile, Paul's childhood friend-turned-Victoria's Secret model, Rhea Durham, invites Paul and a guest backstage at the Victoria Secret Fashion Show. Stuart is the lucky attendee and is shocked to find out that Rhea has been in love with Paul all these years, but Paul is not interested. Also, on two hours sleep, the mayor must meet with the head of the teacher's union for her endorsement.
The Mayoral race hits a snag when Mayor Winston's opponent suffers a heart attack which forces him to drop out of the running, but his wife, Nancy Wheeler, steps in to take his place and surges in the polls due to an outpouring of sympathy. Meanwhile, Charlie gets punched in the face by Caitlin's new love interest and she makes him promise to be the bigger man by not fighting back.
Charlie endangers his relationship with Jennifer when he realizes that he loves his staff more than her. The Mayor decides to propose to Claire, but she says no because he's in the public eye and must be dishonest. This causes problems, because it's Election Day, and a truth-telling campaign by the Mayor could jeopardize his re-election.
Caitlin makes plans with the City Hall Santa without knowing what he looks like. Stuart wrestles with his feelings when he realizes that he's in love with Michelle. And Charlie must decide which staff member is most deserving of a nice new office.
Caitlin finds love with an older man, Tom -- whose daughter, Tracy, flirts with Charlie. Meanwhile the Mayor is depressed by the anniversary of his mother's death, but Carter introduces him to a woman, Christine, who cheers him up in more ways than one. Later, though, Carter reveals that Christine is the receiver of the Mayor's mother's donor heart, potentially threatening their relationship.
Caitlin surprises Charlie on his birthday by inviting his father, Ray, for a visit. What no one knows is that Ray is a con man who abandoned Charlie as a child, and who's about to con his way through City Hall as well. Meanwhile, Paul makes every effort to comfort Carter about Rags, who has passed into the great doggy beyond.
The Mayor's niece, Stephanie, pays a visit to City Hall and flirts with Charlie, who reciprocates - until he finds out who she is. Somewhat later he and Caitlin are caught in a compromising position in the Mayor's bedroom, trying to cover up for Stephanie's wild ways. Meanwhile, Mayor Winston and Carter get trapped in a car for hours, leading Carter to vow to give up his materialistic ways if they are saved, and Paul becomes a contestant on the popular dating show, ""Blind Date.""
When Carter is unexpectedly called to a late-night meeting, Charlie's left in charge of entertaining Spencer, a 16-year-old boy whom Carter sponsors through the ""Big Brother"" program. Having already had a date planned, Charlie has no choice but to bring Spencer along for the ride. Meanwhile, the Mayor is racked with guilt which is causing him insomnia.
Charlie has a hard time keeping up with Tracy, his new 23-year-old girlfriend who likes to party every night. Caitlin and Paul join them at a club one night and they are all arrested after one of Tracy's friends is caught with marijuana. Meanwhile, the Mayor is invited to a fund-raising gala by a very prominent member of the gay community, Martin, whom Carter has a crush on. Both Carter and Stuart also attend, and Martin hits on Stuart who is clueless to his advances, though they feed Carter's jealousy.
Caitlin takes a trip down memory lane and realizes that she and Charlie met years before and that he was the reason why she lost what might have been the best relationship of her life. Flashback to a preppy and conservative Caitlin and a cool, life-of-the-party Charlie at an old college bash. The flashback makes Caitlin realize that her current boyfriend, Tom, might not be right for her, and she ends up kissing Charlie! Meanwhile, the Mayor bartends at a fundraiser at which Paul is trying to pick up a woman, and the woman's friend has fallen for Carter, who is gay.
Caitlin is confused by the kiss she and Charlie shared and seeks the advice of a therapist. Meanwhile, the Mayor buys the staff palm phones which enable Charlie to accidentally eavesdrop on Caitlin's session. He decides to try to fulfill Caitlin's fantasies, which in turn prompts her to decide between Charlie and her current boyfriend, Tom. Paul appears on a controversial radio talk show with Carter feeding him answers.
Caitlin ends her relationship with Tom and tells Charlie she's interested in dating him. When they go out on their first date, things are awkward... until they end up in bed together, that is. But are they ready for a real relationship? Meanwhile, the Mayor hires a temp, Pete, to fill in for Stuart while he's out, but Paul and Carter see him as a threat.
Charlie and Caitlin struggle to find security in their new relationship. To spite Charlie for downplaying an encounter with an ex, Caitlin accompanies one of New York's ten sexiest men on a business date to make Charlie jealous. Meanwhile, the Mayor plots a way to one-up his rival, the Mayor of Los Angeles.
Charlie and Caitlin are caught having sex on a surveillance camera in the Mayor's office and their secret affair is blown. Carter is finally granted a foster child, but is frustrated when he sees that Paul is better with the baby than he is - until the Mayor helps him tap into his paternal instincts.