One of the members of Eric's congregation, Mrs. Bink persuades him to investigate the real reason of why her best friend Mrs. Hinkle is moving into a retirement home. Meanwhile, Simon and Ruthie are performing an experiment and are trying to convince Matt that Simon is shrinking, but the tables suddenly turn for Simon. Also, Lucy tries to get to the bottom of one of her classmates, Shelby as she is rumored all over school of being bulimic.

Mary coerces Matt into asking his friend Brian (guest-star Jason Behr) to take her out on a date despite his lack of interest in her. Although, things begin to heat up between the two kids while on the date---but ultimately ends in disaster after Mary finds out the truth. Meanwhile, Lucy is invited to a sleepover of popular girls, but Lucy is unaware of the group's real intentions for inviting her. Also, Simon begins to teach Ruthie how to swim without taking lessons. Lastly, Eric becomes convinced he's fat and thinks he's getting away with cheating on his diet.

Simon sees his teacher push a man who was screaming at his son. He then feels guilty when he learns his teacher got fired. Annie takes piano lessons as her ""pregnancy project."" Meanwhile, Matt makes a move on one of his college teachers. It turns out he misunderstood her signals. Mary and her friends skip a boring class and get caught. Also, Lucy forgets her lunch in geometry class and finds her teacher eating it--- two days in a row. She and her friend Shelby then learn a good geometry lesson. Lastly, Ruthie has trouble finding the perfect instrument for music class.

Eric worries about Matt as Heather's wedding approaches. Eric learns that his sister Julie is dating Dr. Hastings (the doctor who delivered the twins and almost killed Matt at birth) without telling him or the family. Also, Lucy and Simon are both in their awkward love triangle between all of their two best friends and lovers. Ruthie wants to be a bridesmaid and a bride at Heather's wedding.

In the third season finale, Eric counsels an engaged couple facing difficulties. Mary, Lucy and Simon learn the repercussions of forbidden love, especially Simon when he is caught in his bedroom alone with Deena kissing near his bed. Julie gets married to Dr. Hastings (Hank) and learns that she's pregnant. Also, Heather breaks up with her fiance after she learns he was cheating on her with another woman. Matt tries to save his relationship with Shana after he ran off with Heather, and does this through his pleading of forgiveness.

Mary and her basketball teammates are upset when their high school coach imposes a lockout on the season, citing that their studies should be top priority. When the school calls a meeting to discuss the situation, Eric and Annie support the coach's concerns and decisions. Outraged by the apparent betrayal, Mary and some members of the team break into the gym and vandalize it. They are soon caught by the police and are arrested. Meanwhile, sparks fly when Simon is caught making a lewd hand gesture in front of the school, and is busted. Also, Matt contemplates returning home and Ruthie obsesses about being one of the guys.

The Camden family rallies together after Mary's arrest. Mary truly learns the consequences of her actions after she learns that she is losing her scholarship to college, faces possible school expulsion and jail time. Eric and Annie enlist the help of a lawyer who manages to get Mary enrolled in a community service program. Simon and Ruthie feel overwhelming pangs of guilt for having some knowlege of Mary's intentions and not telling their parients about it. Simon and Ruthie decide to visit many different houses of worship to attain atonement. Also, Matt moves back home to help with the family, but soon realizes he needs to live on his own.