The show centers around Mackenzie Spencer Allen (Geena Davis), the first female President, and her family. In the pilot episode she is serving as Vice-President under the Republican Teddy Bridges, who suffers a fatal stroke. Allen is an independent (she had been a moderate Republican during her brief congressional career, but had left the party), and learns that Bridges had wanted her to resign in the event of his death so that the ultra-conservative Republican Speaker of the House, Nathan Templeton (Donald Sutherland), would become President instead. Allen refuses, becomes President, and then has to deal with all those pesky problems that come with the office.
Episodes would generally trace a political problem and one or more family ones. The cast list is split between staff (Allen's chief of staff, the speaker and his chief of staff, and a few others) and family (the First Gentleman [i.e. the President's husband], their three children, and even the president's mother). Political plot lines in the show include things such as torture, hostages, and so on. Family plot lines involve the First Gentleman's difficulty with his wife being the leader and their teenage children's sexuality.
There were, of course, many comparisons with The West Wing, that other TV series about a U.S. president (which was enourmously popular, critically acclaimed, and tied for most Emmy-award-winning show of all time). Commander in Chief focused more on the president's family, which was only an occasional theme on The West Wing, and there were numerous other differences. However, the comparisons were generally not favorable; The West Wing was ending its run the same time Commander started, and many viewers were probably just disappointed that Commander in Chief was not, technically, The West Wing.
Commander in Chief was cancelled before its first season was complete; it ran for 18 episodes. Changes in producers and time slots are evidence of some difficulties with the show and its audience. Interestingly, it was the #1 show on Tuesday nights until American Idol took that honor, and the #1 new show of the season until Criminal Minds took over that slot. Its direct competition in its time slot was with House.
- Alternate History: The universe of Commander in Chief branches off from real history at some point. There are references in the first episode to the Clintons (Bill and Hillary), Al Gore, and Dick Cheney, all as having held the offices that they did in real life. So the show happens sometime after George W. Bush's first term. More than that is never clearly explained.
- Artistic License – Law: The writers sometimes vastly overestimate the President's legal authority:
- In "First Scandal," Mac issues an executive order creating a scholarship program for college students who agree to become public school teachers. Such a program would require a law to be passed by Congress; the President's executive orders only apply to the inner workings of the Executive Branch.
- In "The Mom Who Came to Dinner," Mac agonizes over whether or not to commute the death sentence of a woman who was convicted of murder in Texas. In reality, the President's pardon power only applies to federal crimes.
- Artistic License – Law Enforcement: In "Ties That Bind," Mac essentially federalizes law enforcement in Prince George's County, Maryland, sending in the FBI to investigate murders over which the federal government has no jurisdiction. No, the President can't do that.
- Bratty Teenage Daughter: Becca. Horace becomes a male version sometimes too.
- Captain Ersatz: Vice President Warren Fitzgerald Keating is clearly meant to be one for former presidential candidate General Wesley F. Clark.
- Casting Gag: President Allen's mother is played by Polly Bergen, who played a female president in the 1964 comedy Kisses for My President.
- Corrupt the Cutie: Horace's and Rebecca's classmates are very eager to do this.
- Fictional Country: The series makes reference to the South American country of San Pasquale. Which is not real.
- Fox News Liberal: Or "ABC Conservative" in this case. Mackenzie is mentioned as having been a moderate Republican before becoming an independent. Despite this, she is never seen to have many (if any) particularly conservative/libertarian traits. And although she's mentioned as clashing with the Democrats sometimes, it's rarely ever at the forefront, and we see her having rather pitched and heated battles against the Republicans instead (and indeed, the main Democrat on the show—Keaton—is portrayed much more favorably than the main Republican, Speaker Templeton). It gets to the point where it starts to feel like Mac's former Republicanism is merely an Informed Attribute.
- Gender-Blender Name: Mackenzie "Mac" Spencer Allen.
- Happily Married: Templeton and his wife Sara—it's disarming and almost creepy when compared to how evil Templeton can be when he wants to be.
- President Allen and her husband Rod are also Happily Married, though certain episodes do highlight the tension that sometimes comes between them. They manage to work it out.
- Headbutt of Love: Mackenzie and Rod do this quite often. It's kind of adorable.
- Hollywood Law: In one episode, Mackenzie debates over whether to spare a mentally disabled Texan woman on death row for murdering a cab driver, and she eventually does so. However, the US President cannot grant pardons or reprieves to state prisoners, only federal ones. Some other episodes see her create a scholarship program through executive order (Congress would have to enact it) and federalizing law enforcement in a state county (which is completely illegal).
- Idiosyncratic Episode Naming: Until Rod Lurie was replaced as showrunner by Steven Bochco, the episode titles began with "First."
- Iron Lady: President Allen.
- Mama Bear: The media corps really gets the idea when President Allen tells them to stay away from her kids.
- Manipulative Bastard: Templeton.
- Never a Self-Made Woman: Invoked when Mackenzie, upon assuming the Presidency, can't have her husband as her chief of staff because she knows that if she did, a not-insignificant number of people would assume that he was actually the one calling the shots. Though Rod isn't happy about it, their marriage is strong enough that it doesn't shake them as a couple (and he knows she's right).
- Nice Job Fixing It, Villain / The Dog Bites Back: Allen would have probably tendered her resignation and allowed Templeton to assume the office (albeit with extreme reluctance), had the latter not been so excessively vocal about his various prejudices while the former was weighing her decision.
- Oh, Crap!: When Templeton hears the tape, his expression is this.
- Old Shame: In-Universe, President Allen gets hold of an old tape from 1965 of Templeton advocating segregation in order to secure election in the South. Templeton is horrified, saying that at the time he was willing to say whatever needed to be said in order to get elected, and that it's not really what he believes, claiming his political record shows this.
- Our Presidents Are Different: President Allen is equal parts President Minority, President Iron, and President Personable.
- Templeton briefly becomes President Scheming when Mac is hospitalized for a burst appendix—they invoke the 25th Amendment and Templeton takes on the duties of the president for a little less than a day.
- Politically Incorrect Villain: Templeton is a bit of a sexist. However, as time goes on, his sexism becomes less and less an example of why he is Wrong in comparison to everything else that he does.
- Scylla and Charybdis: President Allen is often torn between her duties as President of the United States and her duties to her family.
- Shout-Out: Ami's Halloween costume included Starfire's clothes and Raven's cape. Also, her Dad once carried her to give her the sensation of flying. He said She's a bird! She's a plane!
- Statuesque Stunner: Geena Davis makes an elegant, yet extremely tall and intimidating, President Allen.
- Trademark Favorite Food: Templeton and his soft-boiled eggs. Also Amy and her ice cream, donuts, cupcakes, cookies, chocolate-chip pancakes...
- 25th Amendment: Section 1 came into play with President Bridges' death, turning Vice-President Allen into the new President. That also brought up Section 2. With Mackenzie Allen becoming President of the United States, she had to appoint someone for her former position as Vice-President. Not to mention the brief time Nathan Templeton was Acting President while Mac was hospitalized.
- 20 Minutes into the Future: The show aired from 2005-2006, but if one pays attention, it seems like the Allen Administration takes place 8-10 years later. There are references to Dick Cheney serving as VP, indicating that in the show's timeline the Bush Administration happened. It is unknown whether Teddy Bridges was elected in 2008 or 2012 however.
- Who Needs Enemies??: President Allen's initial Cabinet, inherited from Teddy Bridges, starts resigning/backstabbing her as they defect to Speaker Templeton's side.
- Worthy Opponent: Over time, President Allen and Templeton see each other as this, sometimes offering each other grudging congratulations when one of them does something well.
- Your Approval Fills Me with Shame: In the fourth episode, President Allen is disgusted with herself after Nathan Templeton congratulates her on her ability to "understand the burden of the necessary evil" after she accidentally orders a terrorism suspect tortured for information, thinking that she was finally showing the backbone to get the job done (she told the Attorney General, "I don't want to hear about any torture", and the Attorney General interprets this to mean "go ahead and torture him, but don't tell me about it" when she meant "torture is out of the question").