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.
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'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.
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.
Claire gets a job offer from a big hotel chain, but can't tell if Jay wants her to take it or keep working for him. Meanwhile, Phil, Haley and Luke are more interested in Alex's senior "ditch day" than she is; and Manny is dopey from pain killers after having his wisdom teeth pulled, so Gloria seizes the opportunity to get rid of his new girlfriend.
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.