Joan returns home after spending the summer at a 'crazy camp' where she met with a therapist who convinced her that the visions of God were hallucinations. She goes back to work in the bookstore and when God continues to visit her, she denies it is anything more than her imagination. Helen pursues Catholicism by meeting with a former nun who bucks the stereotype. Grace and Luke are meeting in secret and he has signed a contract to not reveal their relationship to anyone. Will learns that the kid who was driving when Kevin was paralyzed in the accident is suing them ...
Still struggling between believing in the visions of God and thinking they are hallucinations, Joan's friend Judith from camp transfers to Arcadia High. Judith decides to throw a party since her parents are out of town, but her attempt to merge with Joan's group of friends goes awry. Grace and Luke try to agree on music and have a difficult time finding 'their song'. Kevin goes to visit Andy to see whether he's really as distressed as the lawsuit contends. Meanwhile, Will is looking for anyone to come forward to tell who shot a young boy, but everyone seems scared to ...
Joan is concerned about Judith hanging with a bad crowd and skipping school. For a physics assignment, Joan begins cultivating a garden near the bleachers, with little hope that anything will grow. Slowly, she gains the support of her friends - even Judith. Helen continues to meet with Lilly, the former nun. Will finds that the death of his shooting witness was arson and that all the fingers are pointing in the direction of his own police force. As his parents try to keep him away from it, Kevin realizes he needs to be more involved with the lawsuit.
Joan is tasked with adopting a cat that is quite hostile, but has to find a new home for it when her mother's Aunt Olive comes to stay with them after having a stroke. Grace and Luke are still keeping their relationship a secret, but things move forward when she decides to confide in him.
It's time for the class president to be elected and Joan takes the side of Brian Beaumont - the guy who kicked her off the yearbook staff - becoming his campaign manager. But she has to decide how far she is willing to go for a victory. Helen battles with a students' objection to an art piece that contains the shellacked remains of a pet gerbil. Will asks Kevin to investigate the new police lieutenant.
Buoyed by an excellent economics test, Joan decides to help her Mom with the church's clothing drive. When she finds some high end donations, Judith suggests they sell the items instead of giving them to the church. At first, they do so and buy more items with the money, but when Joan decides that Adam could free up some time if he had a laptop that Friedman is selling, she keeps some of the money. Helen purchases one of the items and is accused of having stolen it from the clothing drive. Kevin decides to try doing comedy at an open mic night after he bumps into Beth...
Adam is struggling to get his work done while working with an internship at a graphics company. Joan is just as busy with schoolwork and doesn't have time to help with his sculpture, so Judith helps him instead. When Joan gets a video camera and begins filming her family and friends, she captures Adam and Judith hugging, but without sound, she misinterprets their intention. Helen gets a phone call from an old college flame and is tempted to meet with him, but feels guilty about it. Kevin and Will go golfing with Lucy, Will's Leiutenant, who shows interest in helping ...
Luke invites Grace to a cult film showing, but she wants him to attend an anarchist meeting with her instead. While Judith is trying to get Joan to master juggling for a physics project, Adam is planning a romantic dinner out at a swanky restaurant. While he and Joan are enjoying dinner, Judith is hanging out with her old crowd which leads to serious trouble.
The Girardis all give statements about the night of the accident for the court case, which brings back lots of memories. Joan fails her physics test and is told that she is not suitable material for a 4-year college. With all the things going on, it appears that Luke's birthday is going to go by unnoticed.
It's time for Grace's Bat Mitzvah and Luke is having trouble deciding what gift to give her and Friedman's suggestions aren't helping. Joan and the others are excited about it, but Grace is hesitant because of her mother's drinking. Will is trying to investigate Judith's stabbing, but the witness doesn't want to talk. Adam thinks they should talk with the grief counselor at school, but Joan doesn't want to, even though she is struggling with Judith's death. Kevin checks in with Beth, who is about to give her deposition for the court case.
Joan keeps having dreams where Judith appears. God tells Joan to do something she is afraid of, so she tries out for the diving team, because she is scared of heights. Grace tells Luke he hides with his science and will never take risks, so he decides to try out for diving as well, something he has always been scared of. Neither of them are particularly successful in their first attempts. Helen invites the kids to go along to the cemetery to see the headstone put in place for Judith, but Joan resists. Kevin and Beth go on a date and he admits he's falling for her all ...
Things seem to be going well for Kevin and Beth, but when he pushes for more, she isn't so sure. Joan finds that she has an innate talent for Rock, Paper, Scissors and it drives Luke and the other brainiacs crazy. She goes to a guidance program for the non-college track students and decides she'll pursue interior design school. When she goes along with Adam to a college interview, she meets Roger who says he can tutor her to help her get into college. Will is mad when Lucy makes a move that jeopardizes the case against Judith's killer.
God tells Joan to try out for the chorus of a zombie musical at the school. Adam is recruited by the director to build a set for the production. All the students are frustrated with the constant changes by the director. Grace finds it difficult to work with Glynis and Luke in study group. Kevin runs into Andy who tells him he has ended the law suit, but his parents kicked him out of the house. Will is still angry that Andy's family had even filed the law suit in the first place and tells Kevin to stay away from his former friend.
Joan saves one of the mean girls at school from being hit by a truck and suddenly becomes popular. Kevin uses the opportunity to do a TV interview with Joan as a tryout for the local news. The student tries to befriend Joan afterwards, but during an award presentation, she will not confirm whether Joan saved her life. Will becomes increasingly suspicious of Lucy's interactions with him and his family. Luke studies for his driver's license test while Grace objects to cars for environmental reasons.
Adam hires an attractive girl as an assistant, but when Joan begins acting jealously, Adam reminds her of the time she's spending with tutor Roger. Meanwhile, Joan is daydreaming during classes about the possible future between she and Adam. Lucy's advances toward Will are being noticed by others on the force, as well as Helen. Kevin asks Lilly out on a date, but it doesn't go very well.
Joan and Adam want to go to a concert and sleep in his car before coming home the next day, but Joan's mom says she can't go. Joan argues, telling her mom she isn't a little girl anymore and goes anyway, in secret. The night in the van causes tension between Joan and Adam. Kevin tries to help Andy get a job, but finds out just how much the accident still haunts his friend. Friedman rejects a girl who keeps flirting with him, but Luke thinks he's crazy to do so.
Adam believes Helen is treating him differently since Joan spoke with her about their experience at the concert. God tells Joan to help Stevie, but when she starts to look into the issue, Stevie's whole family is shaken up. Kevin has a call back for the TV station, but he is unsure about the story they want him to cover.
Joan is sentenced to community service after picking up an egg carton and being accused of egging the principal's car. She finds out Adam lied to her about a college visit and they argue. Lilly is in charge of the community service and Joan is surprised how much the former nun is doubting God. Luke is upset when he doesn't win a physics award, but is inspired by a fellow scientist when he fills in for Joan at the bookstore.
Helen goes to see Lilly again to restart studying the catechism, but is uncomfortable with Lilly dating Kevin. God tells Joan to get involved with the mock trial where she ends up the prosecuting lawyer against Grace, who is the defending lawyer for Adam, playing Jack (as in 'and the Beanstalk'). However, when she begins to suspect something has happened affecting their relationship, she drills him with pointed questions during the trial. Meanwhile, Will is investigating the kidnapping and murder of a young girl, but is suspicious when a man confesses.
God tells Joan it's time to do some cleaning so she decides to give Adam all the stuff back from their relationship, but it doesn't really make her feel better about their break-up. At school, she tries to help the counselor fight accusations that he has been inappropriately involved with female students. Grace buys Luke a leather jacket and he begins to carry himself differently, but the way he changes makes her uncomfortable. Helen finds out that Kevin is considering getting his own apartment and freaks out, but Will just doesn't understand.
Joan becomes convinced that she and Adam can't successfully be friends after the break-up. Adam takes off on a hike, but everyone is worried when he doesn't return and a storm hits. Friedman convinces Luke to try weed, but it doesn't go well. Helen is contacted by a priest who tells her the man who raped her years ago is terminally ill and wants to see her to apologize.
Joan was suspicious of Ryan from the moment he walked out of the woods with Adam and now he confirms that he has also had contact with God. However, Rayn chooses to use his free will to defy God. Joan is told by God to prepare for her biggest test ever. She becomes convinced that Ryan is responsible for burning down the church and synagogue. As he works into the good graces of Will, Adam, and Helen, Joan fears she won't be able to stand against him. Helen believes her dreams are visions when they seem to predict the church and synagogue fires, but Lilly is skeptical. ...