| Season | Episode | Airdate | Episode Title | Story Line |
| 06.01 | 117 | 09/25/2003 | Dames at Sea | Anxiety occupies Will and Jack, who dread they may have had sex together; and spousal jealousy afflicts Grace, who's concerned that Leo is having an affair while on his medical mission in Guatemala. |
| 06.02 | 118 | 10/02/2003 | Last Ex to Brooklyn | Tipsy fashion editor Diane -- Leo's old flame -- has a dinner-party revelation: she once had sex with Will in a college dorm. The news vexes Grace, whose jealousy has an impact upon Leo. |
| 06.03 | 119 | 10/09/2003 | Home Court Disadvantage | Grace and Leo join Karen for a friendly game of tennis at her exclusive country club. A visit with Will's melancholy mom tests Jack's fear of her. |
| 06.04 | 120 | 10/23/2003 | Me and Mr. Jones | Jack lands a speaking role opposite James Earl Jones in an off-Broadway play. Meanwhile, Will and his mother continue their living arrangement, despite a secret desire to part ways; and Grace finds a way to save money at the gym. |
| 06.05 | 121 | 10/30/2003 | A-Story, Bee-Story | Leo does not get what he expects when he turns to Will to help rekindle his love of New York; Karen coaches Jack for the annual gay spelling bee. |
| 06.06 | 122 | 11/06/2003 | Heart Like a Wheelchair | Lonesome Will is embarrassed to be seen in public rolling along with his mom and her broken foot and bumps into a bachelor doing the same with his mother. Meanwhile, Karen tries to track Lorraine down only to discover her father Lyle. |
| 06.07 | 123 | 11/13/2003 | Nice In White Satin | Pressured by Will, Karen decides it's time for her annual Walker corporate physical. Jack finds his true calling--student nursing--and begs Will and Karen to support this new endeavor. |
| 06.08 | 124 | 11/20/2003 | Swimming from Cambodia | A marital crisis upsets Grace, who reluctantly confides in Will after leaving Leo in Cambodia; nursing school flusters Jack, intimidated by a no-nonsense instructor who gets set straight by Karen. |
| 06.09 | 125 | 12/04/2003 | Strangers with Candice | Will catches the eye of a female diner after being stood up; Grace bumps into a man with whom she once shared a forgettable encounter; Karen runs into her nemesis, Candice Bergen. |
| 06.10 | 126 | 12/11/2003 | Fanilow | A Barry Manilow concert enthuses Will, an avid fan not above coming on to a staffer with direct access to the star. Meanwhile, Grace discovers her mother has cancelled their annual shopping spree to have dinner with Jack. |
| 06.11 | 127 | 01/15/2004 | The Accidental Tsuris | Grace's free-loading sister comes to town to launch her latest business enterprise; Karen spurns Lyle's proposals but has a change of heart when Lorraine expresses her disapproval. |
| 06.12 | 128 | 01/22/2004 | A Gay/December Romance | A rich plastic surgeon tries to buy Will's affection; Grace boycotts a new restaurant. |
| 06.13 | 129 | 02/10/2004 | Ice Cream Balls | Will's slightly eccentric new client falls for Jack, who refuses his advances. Meanwhile, Grace and Karen discover hidden money while trying to fix the plumbing in Leo's cabin. |
| 06.14 | 130 | 02/19/2004 | Looking for Mr. Good Enough | Will is the only single man in a cooking class full of couples, including Jack and his new boyfriend; Karen's mother asks Grace to decorate her apartment. |
| 06.15 | 131 | 02/26/2004 | Flip-Flop: Part One | Will and Grace begin a business venture selling apartments; Jack runs into his former acting mentor, Zandra; Karen and Lyle try to renew romance. |
| 06.16 | 132 | 03/04/2004 | Flip-Flop: Part Two | The Karen-Lyle affair founders, thanks to willful Lorraine; the Jack-Stuart liaison loses luster, giving Will and Grace a chance to resell the guys' apartment for a much higher price. |
| 06.17 | 133 | 03/11/2004 | East Side Story | Will and Grace clash with lesbian apartment flipper champs. Meanwhile, Karen seeks the spiritual guidance of psychic John Edward. |
| 06.18 | 134 | 03/18/2004 | Courting Disaster | Speeding lands Karen a ticket from a stoic cop, whose court appearance holds a surprise for Will. Another revelation stems from Jack's mistrust of Stuart, espied in a movie theater with a much younger fellow. |
| 06.19 | 135 | 03/25/2004 | No Sex 'n' the City | Will makes the mistake of taking Grace's advice on love, playing hard-to-get with his new pseudo-boyfriend. Meanwhile, Jack and Karen despair after learning their favorite TV series will be going off the air. |
| 06.20 | 136 | 04/01/2004 | Fred Astaire and Ginger Chicken | Grace meets Vince, but abruptly leaves shortly after; Jack auditions replacements for Karen because he thinks her marriage will end their friendship. |
| 06.21 | 137 | 04/08/2004 | I Never Cheered for my Father | At Tina's urging, Will tries to find out if there is a new woman in his father's life. Meanwhile, Elliot asks for Jack's help when he tries out for the high-school cheerleading squad. |
| 06.22 | 138 | 04/22/2004 | Speechless | On the eve of his graduation from nursing school, a nervous Jack turns to Will for help writing his commencement address. |
| 06.23 | 139 | 04/29/2004 | I Do. Oh, No, You Di-in't | Karen and Lyle fly to Las Vegas to elope. Meanwhile, Leo returns from Cambodia. |