Grace and Jack's temperamental mother/son relationship takes a dangerous toll on Bobby as he gets caught in their rival forces, prompting a major change in the McCallister household. The arrival of a new college president, Peter Benedict, and his beautiful daughter, Courtney, makes an impression on the McCallisters that lasts a lifetime.

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 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.

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.

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.

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.

Bobby's relationship with Dex continues to grow until Grace walks in on them kissing in her study. After failing to convince Bobby to break it off with Dex, Grace and Jack take matters into their own hands. Meanwhile, Peter shows his overprotective side and though he has Courtney's best interests at heart, ultimately causes her embarrassment among her peers. Also, the future reveals that President McCallister has trouble with his oldest son and the secret service.

Peter is forced to take action after learning about the relationship between Grace and Tom. Meanwhile, Bobby and Warren decide to make some cash by doing yard work in their neighborhood and are shocked when they come across Jack's wallet in a neighbor's garage. After learning that his wallet was discovered and realizing who jumped him, Jack and Marcus take matters into their own hands.

Jack and Katie's relationship progresses, while Courtney's comes to a screeching halt after Jack discovers Nate is cheating on her with another girl. When Bobby is required to do a family history project for class, he goes through his mother's closet for clues about his family and discovers a letter that reveals the real reason his father left. Meanwhile, Grace is shocked to learn that her affair with Tom has cost her more then she had bargained for.

Jack explodes after catching Grace smoking pot again and gives her an ultimatum. However, after a particularly trying day, Grace seeks refuge in her old habit and is unprepared for the price she must pay for the one joint. Meanwhile, Bobby tries to help make things better for Jack, both with Courtney and in school, but only succeeds in making things worse. Also, it is revealed how President McCallister became affiliated with a surprising political party.

Bobby joins the "challenge program" at school and learns a powerful lesson. Meanwhile, Grace is startled by news that Bobby's new teacher gives her regarding Jack. Also, the flash-forward segments reveal how a surprising ally helps President McCallister out at a critical moment in his political career.

The future reveals a dark secret about the first lady. Back in the present, Jack offers to escort a depressed Courtney to her father's work fundraiser leading to an unexpected confession and kiss. Meanwhile, much to the consternation of her sons, Grace offers to let a homeless man stay at their house for a few days until she can find him a better place to live.

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 and Bobby discover that Grace plans to visit their father, Juan, in a Texas prison. Bobby insists on joining her and the three embark on a spontaneous road trip, where Grace is forced to reveal the shocking reason their father is in prison. The future reveals Jack's heartbreaking fate and details Bobby's unlikely road to the Presidency and, for the first time, we hear the voice of President McCallister.

Bobby is heartbroken over his break-up with Dex and decides to get even with Jack after finding out he is responsible for their split. Bobby's actions cause Jack, Missy and Courtney much embarrassment and anger, which results in a feud between the brothers. Meanwhile, Grace and Tom sneak away from the campus election night party to smoke pot, which proves to be a terrible mistake for Grace and her family. The future reveals that in 2040, McCallister wins the election by only a few votes.

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.

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.

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.