Cameron isn't ready to conclude his honeymoon with Mitchell after their wedding. Gloria takes Jay to task over his appearance. The Dunphys must ready themselves for the return to school.

Phil, Luke, and Haley cause nothing but aggravation for Alex when they tag along on her tour of Caltech. Jay and Gloria have trouble finding the perfect gifts for their anniversary.

The Dunphys are down with a cold, thanks to Phil. Jay and Gloria try to help Manny deal with playing football, and Cameron doesn't know how much playtime to give him. Mitchell debates with Lily's new friend, Sydney.

Things become tense when the Dunphys temporarily move into a hotel, Gloria is suspicious of Manny's new girlfriend, and Mitchell discovers that he has jinxed Cameron's football team.

The Dunphys try to persuade the perfect couple to move in next door, Manny dates the daughter of Jay's biggest nemesis, and Mitchell and Cameron try to get Lily a new teacher.

Phil takes over Halloween decorating duties from Claire. Jay is upset when he wants to dress up as Prince Charming but Gloria buys him a Shrek costume. Mitchell has a problem in court with the stenographer working in a scary costume.

Haley and Andy start spending a lot of time together. Gloria wants Manny to learn Spanish at school instead of French, and a reporter takes more than a passing interest in Cameron and Mitchell's lives.

Phil and Luke take over Thanksgiving duties but Claire readies an emergency plan. Jay and Gloria get their holiday plans interrupted and regret not telling anyone. Cameron has to think of a way to get Lily to wear a dress for dinner.

Jay and Gloria try to get out of parties they must attend. Mitchell's kind gesture to a co-worker backfires on him, and Phil and Claire think Alex is lying when she tells them she found a boyfriend.

Claire and Gloria hang out with Haley on her 21st birthday. Alex, Luke and Manny babysit Lily and she decides to drop the ‘where do babies come from?’ bomb.

A near miss from a crash has everyone in the car either on edge or adopting a new carpe diem mentality.

Familien Dunphy er trætte af, at naboernes båd spærrer for indkørslen, og derfor inviterer Phil sin far og hans pensionerede venner til at hjælpe dem med at sætte Ronnie og Amber på plads. Imens bliver Jay og Gloria uenige om Joes pottetræning, og Cameron tager Lily med på klovneskole uden at fortælle noget til Mitchell.

Da Phil tror, at Luke har givet ham den kolde skulder, bliver Andy Phils nye højre hånd. Imens står Jay med et dilemma, om han skal skille sig af med hunden Stella, fordi Joe måske er allergisk overfor hende, og Mitchell får rollen som kontorets populære fyr.

Claire believes that Phil could be more into "Juliana" than her. Gloria's sister pays a visit.

Jay shows Manny how to defend himself whilst Mitch and Cam decide to throw Sal a belated baby shower.

Claire does some online snooping that causes drama with the rest of the family.

When their competitor releases a catchy ad, Claire and Jay race to shoot a commercial of their own.

Claire tackles spring cleaning; Haley tries to distract Alex by taking her to a music festival.

Jay's birthday comes with a number of interesting gifts, including Phil's high-tech outdoor grill, and Claire and Mitchell's offer to pay back some ancient loans—though they don't think he'll actually accept it. Meanwhile, Gloria teaches Manny and Luke a lesson about drinking; and Andy finds himself in an awkward situation when Haley brings her new doctor boyfriend.

Jay agrees to sub in on Cam's bowling team, not knowing it's an all-gay league. Phil and Clair have an unexpectedly nice time with their neighbors. Gloria and Mitch agree to go out with Haley.

Jay and Phil try to stand up for themselves on the home front while Haley attempts it at work.

Alex learns she has to share valedictorian honors with a rival, but the tie could be broken by a 1-mile run for a gym grade neither has completed. Meanwhile, Gloria studies for her U.S. citizenship test, but is distracted by a visit from Javier; and Mitchell and Cameron join a protest against a restaurant where they actually can't wait to dine.

The sixth season ends with Alex's graduation party at Jay and Gloria's house, but Phil is stuck in Seattle on a business trip, so he uses the latest in technology to be as close as he can get. Meanwhile, Claire worries about Alex's gift, Jay complains that Gloria's cousin has overstayed his welcome, Mitchell keeps the news of his layoff a secret from Cameron, and a visit from Andy's girlfriend turns Haley's world upside down.