Grace is accused by Hebba, an Arab-American female student, of letting her individual beliefs about religion color her lectures. Taking offense, Grace chastises Hebba in front of the class, which leads to a boycott of Grace's classes by the religious groups on campus. Meanwhile, after helping Warren with his bar mitzvah and learning a bit about Judaism, Bobby demands to know why Grace never took him to church. Completely thrown by the accusations, Grace must explain to Bobby & Hebba what "faith" really means to her. Also, Jack helps Marcus out of tough situation.

Grace is stunned after Benedict informs her that her fellow colleague and good friend has been accused of sexually harassing a student. Grace immediately defends her co-worker but must re-think her loyalty when new evidence arises. Meanwhile, Bobby is spending so much time with his new girlfriend, Dex, he begins to neglect his school work. Under pressure from Grace to succeed, Bobby cheats on his test. Still reeling from the guilt of kissing Courtney, Jack is horrified to discover she and Missy have become friends.

Grace promises to be on her best behavior when she and Jack go to Missy's house for dinner but loses her cool after the Reverend starts attacking her ideals. Upset by the event, Grace turns to Tom and the two share a romantic moment. Meanwhile, Bobby intentionally loses at chess games with Peter in order to spend more time with him. Also, Courtney uses Marcus to get back at Jack.

Grace's warm, intelligent, gay younger brother makes a surprise visit to the McCallister home for Thanksgiving. Grace is thrilled that he has returned but her feelings change after he lands in jail on drug charges. Meanwhile, Jack feels responsible for a friend's suicide.

Jack is mortified after Grace catches him buying condoms in preparation for his big night with Missy. Trying to be supportive of his actions, Grace insists that Jack talk to her about sex and questions him about whether he is sure Missy is the right girl. Meanwhile, Jimmy slips back into his old habits, forcing Grace to make a difficult decision about her family. Also, Bobby tries to help Warren win over his crush Deena but is surprised when she declares she has feelings for Bobby.

Jack tries to resume a sense of normalcy after his brutal attack, but finds that the injury may keep him from returning to his old life. Grace is blackmailed by a student who caught her leaving Tom's room, and Courtney meets a new guy who captures her interest. The future reveals President McCallister's unique actions after a horrific bombing in Chicago.

Uh oh. Bobby becomes suspicious of Grace's relationship with Tom after Tom coincidentally shows up during a camping trip. While Jack and Missy's relationship seems to be dying a slow death, Courtney's dating life is picking up steam with college freshman Nate. The future reveals that President McCallister, despite risks involved, supports space travel to the planet Mars.

Jack walks in on Grace and Tom in a compromising situation and tells Grace he disapproves of her romance. Meanwhile, Bobby convinces Grace to allow him to attend an overnight hunting trip with Peter, which proves to be an eye-opening experience for Bobby.

Grace and Tom's relationship is exposed when a fellow professor catches them kissing in her office. Later in the evening, Peter turns to Grace for advice when he finds out Courtney is having sex with her boyfriend. Meanwhile, Jack's relationship with Katie progresses and in an effort to become popular at school, Bobby and Warren decide to have sleep over and come up with a shocking idea to make the evening memorable.

Jack finds out that Bobby has secretly decided to try out for the track team and instantly shows his disapproval. Later, Jack finds out that his relationship with Katie isn't what he thought it was and is shocked to find out that Courtney and Marcus may have feelings for each other. Meanwhile, Grace's excitement to be the opening speaker at an event for her mentor turns to disappointment when she is asked not to speak due to her scandalous relationship with Tom.

Missy turns Jack's world upside when she reveals a secret that could change their lives forever. As a result of her actions, Missy is kicked out of her home and turns to Grace for support and guidance. Meanwhile, Bobby surprises Grace by telling her that he would like to be baptized and tries to convince Peter to be his godfather.

After getting into a big argument at the not-so-exciting school dance, Jack, Courtney, Marcus, Missy and Randy decide to drive to an after-party, but a deadly car accident prevents them from making it to their destination. Meanwhile, Grace agrees to chaperone Bobby's school field trip, much to Bobby's dismay, which proves to be a hurtful and eye-opening experience for Grace.

To protect Marcus, Jack tells the police that he was driving the car the night Missy died. The guilt becomes too much for Marcus and he confesses to his dad, who immediately calls Grace. A surprising ally comes to Jack's aid after Grace demands that he tell the police what really happened. Meanwhile, the group's sadness turns to outrage after Reverend Belknap delivers a shocking eulogy at his daughter's funeral. Also, Bobby feels betrayed by the fact that Warren is moving to Chicago.