After Jay attends the Academy Awards, Gene Siskel and Roger Ebert break up and each rope Jay to be their new partner.

Jay's boss, Duke, has just made a new invention, "Phillips-o-Vision" which alters movies to make them more "like-able". Jay is disgusted with Duke's invention but when Duke is discovered to have a fatal disease, Jay must find a cure for Duke's ailment.

Jay befriends his make-up lady Doris after they attend a musical adaptation of The Hunchback of Notre Dame, and thinks that she may be the mother who gave him up for adoption years ago.

Jay celebrates his 1000th episode but the episode is less than successful. Ratings get worse so Jay seeks image consultant, Adolph Hitmaker, for advice. The advice is unsuccessful and Jay is fired. Jay gets a new job on a show which teaches English for cab drivers but Jay is unhappy so he decides to win himself another Pulitzer Prize.

Jay's ratings are not doing very well and Duke is about to fire him so Jay is feeling depressed. His feelings become better when he meets a new girlfriend named Alice and her daughter Penny. Alice gives Jay tips on how to improve his show and her advice works. Jay wants to get to know Alice better but discovers she has a boyfriend whom she wants to reject but can't.

When Jeremy Hawke's sister, Olivia Newton Hawke, visits New York, Jay meets her and is smitten with her which puts his relationship with Alice on the line when she begins to feel left out. So Jay then must decide who he really loves.

When Jay helps Marty become class president, Duke decides to have Jay help him become US President.

Jay is hosting his 10th anniversary show held at Carnegie Hall where he showcases a number of movie clips from old episodes such as Jurassic Park 2, Every Which Way but Lucid, and Rabbi P.I. The show is later held hostage by a number of terrorists who threaten to blow the place up with a bomb tied to Jay's waist. Fortunately, everybody is eventually rescued by Milton Berle.

Jay and Marty begin to feel a little big so they enroll in a weight loss camp. Marty loses a remarkable amount of weight which makes him feel more self- confident but when he is placed as the star in a school play, he doesn't feel his skinny self is right for him. Meanwhile, Jay receives a death threat from Belgian actor Jean Paul Le Pope whose movie he panned.

Alice's sister, Miranda, comes to visit them which Alice is not comfortable with. Miranda must find work in New York so she joins "Mattress in an Hour" delivering mattresses. When everybody attends a party held by Duke, Miranda falls in love with Duke but is shy because of a wrinkle. She runs out on Duke at midnight and Duke must find the woman who fits her slipper. When it turns out to be Doris, Jay must get Duke and Miranda reunited.

At Marty's slumber party, Jay is asked to tell his story in which he got caught up in the Gulf War. Jay tells how he was attending an Iraqi film festival and eventually was thrown in jail where he escaped and lead a troop of men across the desert.

Jay is considered to be one of the most unpopular men on Earth (ranking even worse than Adolph Hitler) so Duke attempts to spruce up the show to get more people interested. When this doesn't work, Jay decides to soften his image by going on the "Geraldo Show" with his mother but Jay gets an even worse reputation when his mother embarrasses him to the point where he tells her to "shut up".

When the studio catches fire during Jay's show, he collapses and must be rescued from the fire by Doris. When the news reports Jay's being rescued, he gets a reputation as being a wimp so he tries to prove his manliness by running in the New York marathon which tends to be more tiresome than it seems.

After Marty fails to win an event at his school field day, he is feeling very low so Jay tries to improve his self-confidence by getting him interested in playing guitar and putting him in the school talent show. Meanwhile, Them Magazine names Jay "the wittiest man alive" so Duke offers to pay everyone who doesn't laugh at Jay's show $100 which doesn't go over very well.