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, noticing everyone in New York has a fiancee except him, begins to feel unloved. Things change when he goes to review the movie, Indecent Proposal II, and falls in love with the projectionist screening the movie. They arrange a date at her house where she is revealed to have an obsession with Jay to the point where she kidnaps him and ties him to a bed holding him hostage.

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

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.

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.

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.

Jay is offered to write the screenplay for a new movie, Ghostchasers III, so he takes a break from his show to go to L.A. to write the new movie and experience Hollywood life but the movie producer isn't satisfied with Jay's script.

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.

Eleanor is determined to have her daughter, Margo, attend the annual debutantes ball as it is a tradition in her family. When Margo is reluctantly forced into it, Jay decides to accompany her. Meanwhile, Jay competes in his time slot against children's idol Humphrey the Hippo.

Marty invites his Jay to career day at his school where Marty develops a crush on a Cuban girl named Carmen. They go on a date but when Carmen decides to fly back to Cuba, Marty follows her and Jay must get his son back.