Joan Girardi has begun acting a little strange since her family moved to the city of Arcadia. No one knows that various people keep introducing themselves as God, and then giving the teenager specific directions to do things. Unsure of what God wants, and if she's even sane, Joan tentatively begins to follow God's cryptic directives, all the while trying to retain a "normal" teen-aged existence.
After a summer of therapy and with school resuming Joan tries to return to a ""normal"" life even as she ignores God, who keeps reappearing; Will is sued for emotional distress by Andy Baker, whose drunk driving caused the accident that paralyzed Kevin; Luke and Grace try to adjust to their relationship.
Judith, a wild friend of Joan's from summer camp, starts school at Arcadia High; Will investigates a drive-by shooting; Kevin confronts Andy about the on-going lawsuit.
After God suggests she be part of a growth process, Joan decides her science project will be to plant a garden in an inhospitable area to see if it can survive.
God has Joan adopt a wild cat; Helen's Aunt Olive has a stroke while visiting; Will calls Internal Affairs to investigate for corrupt cops.
Things get dirty in a student council election as God instructs Joan to support a candidate; Helen must deal with a student who protests another students work of art.
Gods tells Joan to help her mother collect clothes for the homeless; Kevin attempts stand-up comedy in order to impress Beth; Will wants to counter-sue the Bakers.
Joan struggles with the pressures of Junior year; God assigns Joan to work on a videography; Adam and Judith work on a project together; Will, Kevin, and Helen meet with a lawyer to discuss a counter-lawsuit.
After being prodded by Judith to go on a real date, Joan and Adam nervously prepare for a romantic night at a fancy French restaurant. Little do they know that Judith has subsequently made some misguided plans for herself for that evening, which later causes the guilt-ridden Joan to wonder if she could have prevented her friend's misfortune.
As the Girardis are deposed for the lawsuit against them regarding the car accident that disabled Kevin, they look back on their memories of that horrible day.
While helping Grace shop for a dress for the occasion, Joan is delighted to finally meet Grace's seemingly perfect mother, Sarah. However, when Sarah's drinking problem becomes evident, Joan begins to understand why Grace is so private â€“ and why she's long been avoiding having her bat mitzvah. Meanwhile, Luke racks his brain to come up with a meaningful bat mitzvah gift for Grace. Additionally, Adam and Joan have different ways of coping with Judith's death. Will supports Lucy's less-than-legal means of trying to get one of Judith's friends to describe Judith's on-the-run killer, and Kevin's ex-girlfriend is deposed for the trial.
As Joan tries to work her way up to the high dive despite her acrophobia, Luke attempts to overcome his paralyzing fear of undertaking an activity at which he might fail. Meanwhile, Will continues his quest to find Judith's killer, and Kevin goes on a date with Beth. Additionally, while reflecting on Judith's death and Kevin's accident, Helen becomes overwhelmed with concern about her family being in harm's way.
Despite everyone's protests, Joan allows her snobby, Ivy League-educated guidance counselor to advise her against applying to college. However, after Joan relays her plans to Roger, an engaging college student on the campus she's visiting, he tells her that college is attainable and persuades her to hire him as a tutor. Meanwhile, Adam becomes jealous of Joan's rapport with Roger; Will sees a dark side of Lucy; Helen questions her commitment to Catholicism, and Beth finds it difficult to resume a relationship with the wheelchair-bound Kevin.
Joan gets a chorus role in the school musical per God's request and is elated when Adam agrees to design and build the play's elaborate sets.
After saving a girl's life Joan suddenly becomes famous but she soon learns fame is fleeting and can even turn against you; Adam has a job interview that doesn't quite go the way he wants; tension builds between Lucy and Will; as Luke prepares to get his drivers license Grace tries to educate him on the harmful impact vehicles have on the enviroment.
God tells Joan to do an extra credit English assignment on romance poets, which causes her to question her own love life.
Incensed that Will and Helen have forbidden her to go to a concert with Adam and stay overnight with him in his father's camper, Joan goes anyway. After Joan has a conversation with God about free will, she decides to use it as a rationale for lying to her mother in order to go on the trip as she's convinced that Helen simply wants her to remain a dependent little girl. Meanwhile, Luke is shocked when the nerdy, girl-obsessed Friedman rebuffs the advances of the surprisingly infatuated Stevie.
Joan is convinced that she's meant to help Stevie keep her part-time job with Adam, despite Stevie's mother's order that she quit. In an effort to supply Stevie with the Social Security number that Stevie's mother is withholding, Joan gets Kevin to use his investigative reporting skills. Kevin's findings end up leading Will to make a discovery that quickly turns Stevie's world upside-down. Meanwhile, Adam is upset with Joan for telling Helen that he tried to have sex with her, and Kevin is conflicted when the local television station asks him to do a report that pertains to paralysis.
After Price discovers Joan holding an empty egg carton near his freshly egged car, he wrongly assumes she's the culprit and punishes her with a weekend of community service. Without more direction from God than to rise above the injustice, Joan tries to figure out if she's meant to help a bitter former nun, Lilly, who is overseeing the service project, or one of the social outcasts who are serving as a result of their own offenses. Meanwhile, Joan's also upset that her reluctance to begin a sexual relationship with Adam is driving a wedge between them. Also, Adam meets a troubled artist at the community center; Joan gets Luke a job at the bookstore; Kevin has another car accident.
Joan prepares to prosecute a case for a mock trial at school, per God's request, while enthusiastically planning a way to celebrate her one-year anniversary with Adam, who has secretly betrayed her. Joan surprises everyone with her passion in prosecuting a mock case against the equally motivated defense attorney, Grace. Meanwhile, while trying to hide his guilt from Joan as she plans a special anniversary night out with him, Adam decides to confess his wrongdoing to an appalled Grace. Meanwhile, Will investigates the murder of an eight-year-old girl and Helen continues her study of catholicism.
In the wake of Joan’s breakup with Adam, God tells her to do some house cleaning, which puts her in the middle of a school scandal.
Joan and Grace fear the worst when, on the heels of failed attempts to reconnect with Joan, the emotionally fragile Adam goes missing during a hike... Despite Grace's attempts to foster a more comfortable rapport between her friends, Joan is intent on hurting Adam with her rebuffs, which she regrets when it appears that his life may be in danger. Meanwhile, Helen is shocked when a priest tells her that the man who raped her 25 years ago would like her to visit his deathbed so he may apologize. Also, Luke is dismayed and intrigued when he learns that Friedman has been getting stoned.
God tells Joan that the last two years were a spiritual boot camp for her greatest challenge yet, pitting her against a man with a sinister agenda.