Cate has a pregnancy scare with the Hennessy children worrying about a new sibling, while Bridget has a scare of her own as her popularity decreases at school.
Bridget is horrified when Cate is asked to fill in as the sex ed instructor in her daughter's class. But Cate is in for a shock when she tries to answer a student's written question about being pressured to have sex — and realizes it may be from Bridget. Meanwhile, Paul and Kerry are too embarrassed to look each other in the eye after watching a foreign film together that contains a sexually explicit scene.
When Fred and Mary Ellen Doyle ask Bridget to be a part of a video message they are sending to Donny at the Naval Academy, they are shocked to discover that Bridget has broken up with their son on the tape — and Donny goes AWOL to try and patch things up. Meanwhile, Paul is asked to help give a nickname to a neighborhood prankster who has been terrorizing the block, not realizing that the culprit may be living under his own roof.
The Hennessy family has to deal with the tragic death of one of their own, Paul, their beloved father and husband. To deal with the grieving, Cate's parents come while neighbors also try to help the family deal with their loss.
An event is going to be held in Paul's honor, but they need his final article to complete the event. The rest of the Hennessy family goes on a search for the article as they reminisce about their father and try to move forward one step at a time.
Cate is unprepared for the diverse reactions exhibited by Bridget and Kerry on their first day back to school since their father's death. Meanwhile, Jim tries his best to be helpful by making some questionable home improvements to the Hennessy home.
With a little help from Jim, Cate persuades Rory not to give up on trying out for basketball, as Paul would have been proud to see his son on the team. But Rory is torn about the tryouts because he doesn't think he has the right stuff to make the cut. Meanwhile, Bridget and Kerry's decision to stop fighting in honor of their late-father begins to unravel when Bridget accidentally destroys Kerry's collage honoring Paul in tribute.
While Cate plans to raise the family spirits with a special Thanksgiving dinner, Rory takes it upon himself to be the man of the house by looking after Bridget and Kerry when he learns that they are planning to attend a party with their boyfriends on the holiday. Meanwhile, When Cate's mom visits, her father feels he can still save their marriage.
Bridget gets the lead as Anne Frank in the school play and Rory brings home a ventriloquist dummy that the school psychologist recommends that he uses.
The Hennessy family needs to get more active so Cate signs the family up at the local YMCA, which also happens to be the place Bridget works at. Jim, however, is becoming too overprotective and doesn't think that Bridget should work there because too many men are hitting on her. Rory also has to deal with some problems during his Yoga classes.
Cate's nephew C.J. Barnes comes to visit and pay his respects to Paul. C.J., however, can't seem to stay out of trouble when he helps Rory on getting better in kissing girls and takes the blame when Kerry, who only has her permit, not her driver's license, takes Cate's car and accidentally dents it while driving Bridget on a late night errand.
C.J. tells Rory about how he stole his old school mascot, Rory goes out and steals a police dog. Cate is very shocked when she finds out the dog finds marijuana in Kerry's backpack. The reasoning Cate thinks Kerry is doing drugs is because of Paul's death, but finds out is because she wants to rebel against her mother. Finally, Bridget is brought home by a police officer for not wearing a helmet while riding with her boyfriend on her motorcycle, after Cate told her she had to.
Bridget hires Jeremy to tutor her in order to boost her grades to better her chances at being accepted by a good college. But with Valentine's Day fast approaching, Bridget soon finds herself without a date when her boyfriend gets sick, and her friends begin to wonder if Jeremy is taking his place. Kyle treats Kerry to an very un-corporate Valentine's Day celebration, Rory gets pointers from Jim and Cate about the perfect gift for girlfriend Missy, and Jim sends C.J. on an errand that lands him in Canada.
Bridget decides to make a move on her tutor, but discovers that he may have his sights set on her debate team opponent. Meanwhile, after accidentally setting fire to C.J.'s van, Jim is not-so-thrilled when Cate forces him to share his basement room with his now homeless nephew.
After being told that she's fickle when it comes to relationships, Bridget is afraid that she may end up hurting Jeremy's feelings when her ex-bad boy boyfriend, Damian, returns to town. Meanwhile, Kerry is outraged and plans revenge when "provocative" dancing has been banned from the high school formal, chaperoned by her mom and Grandpa, C.J. partners with Rory to broadcast school scandals over the internet, and Jim falls for Ms. McKenna, a member of the high school's PTA committee.
Cate is encouraged to pursue a once-thought-unobtainable dream of becoming a singer. Meanwhile, C.J. and Jim find themselves trying to bond in a bar when Cate encourages C.J. to take his grandfather out after he is dumped by his wife — in a letter — and Bridget angers Kerry by dyeing her hair blonde after she complains that the romance is fading from her relationship with Kyle.
After Kerry is promoted to assistant manager at a fast food restaurant in the mall, Jim is hired to handle the register. But when she witnesses his disdain for the customers, Kerry is faced with the dilemma of having to fire her grandfather. Meanwhile C.J. — who has been employed as a mall cop — busts Bridget for sneaking into a movie without paying, and Cate catches Rory selling worthless family items on the internet under false pretenses.
Cate sends Bridget and Kerry to their grandmother's house for a visit after the Hennessys decide against vacationing at the family cabin. But while on their road trip to grandma's, the girls are shocked to find Cate at their father's favorite saloon with a mysterious stranger. Meanwhile, Kerry makes Rory's life miserable when she discovers that he has a crush on her friend, Rachel.
Upon discovering Cate in the arms of Artie — Paul's successor at the newspaper — Bridget and Kerry decide to blow off their planned trip to their grandmother's and take to the open road to sort out their feelings. But after meeting up with C.J., the girls find themselves at a familiar location that was beloved by Paul. Meanwhile, Rory continues to pine for Rachel, who confesses her true feelings for him.
After discovering that Bridget lied about her whereabouts in order to attend C.J.'s college kegger party, Cate grounds Bridget and banishes C.J. from the house. Meanwhile, Jim is forced to take a written driver's test with Kerry after he's pulled over for reckless driving and carrying an expired license.
After witnessing some strange behavior from Bridget and Kerry, Cate tries to find out what they are up to — not suspecting that they might be trying to set up a special Mother's Day getaway for her. Meanwhile, C.J. and Rory doubt Jim's ability to put an engine back together after he falls in love with a classic car — which is in for a wax job at Rory's new detailing service — and decides to fix a noise in the motor.
When Bridget is busted over a school dress code violation, Cate is called upon to meet with her new principal, Ed Gibb. But Cate is in for a shock when she discovers that she went to high school with Ed — who remembers it vividly — though she doesn't remember him at all. Meanwhile, when C.J. becomes his massage therapist, Jim hurts his feelings when he refuses to admit that his wayward grandson has become good at something.
Kerry is accepted to a trip over the summer to Europe while CJ and Rory double date with sisters Missy and Sissy, although Sissy is currently engaged. Also, Kerry jeopardizes her trip to Europe while having a sit in to stop dissecting frogs.
Cate finds herself in the awkward position of having to deal with Principal Gibb when she forgets to turn in a health form for Kerry's trip to Europe. Then, when she discovers that Bridget took the fall for Kerry for organizing a school sit-in, she agrees meet Principal Gibb again over coffee in order to set the record straight. But the girls are convinced that their mother's innocent coffee meeting is really a date. Meanwhile, Kerry is furious when Bridget is elected student body president and wins a trip to Washington, D.C. because everyone thinks she organized the school sit-in, and Jim's new relationship with Tina irks Cate because she still hopes that her father will reconcile with her mother, on the double-episode season finale.