Joan is saddened when she learns Rocky (Death Be Not Whatever) has passed away, causing her to further question God about life and death. Will loses his job when his discovery, and whistle blowing, of a political conspiracy causes the town government, and police department, to be desolved. While Luke continues to work on his science project and his growing attraction to Grace and Kevin is injured in a game of basketball.

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 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.

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.

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.

Joan gets a lesson in popularity when God tells her to try out for the cheerleading squad, and her efforts to impress two pom-pom girls pay off with an invite to hang out together outside of school. Meanwhile, Will's first case working with Det. Toni Williams involves an abandoned newborn left in a trash bin, presumably by a student from Arcadia High. Another story line has a classmate sensing a gay vibe in Luke.

Joan joins the yearbook staff, per God's request, and decides to use this assignment as a means of impressing Adam... Feeling threatened that Iris and Adam continue to share a bond over their passion for art, Joan vows to discover a hidden talent that Adam will admire. However, her disastrous attempt to be the yearbook's star photographer soon adds to her insecurities about losing him. Meanwhile, Will and Toni attempt to set up a sting for a man who is planning to hire a hitman to murder his wife.

God wants Joan to score an ""A"" on a test about French saint Joan of Arc. As the teen hits the books, she draws comparisons to the life of the young heroine who claimed to hear divine voices and was burnt at the stake. Helen finds her daughter's newest obsession troublesome and urges Will to have the entire family visit a therapist. Meanwhile, Will is unjustly raked over the coals for shutting down a crack house.

God tells Joan to learn to jump rope with a group of inner-city teens, one of whom Joan discovers is homeless. Kevin goes on a date, but not with who you think.

When the hospitalized Joan is diagnosed with Lyme disease, she begins to question if she's been seeing God or merely experiencing the hallucinations that can be symptomatic of her condition... Upon hearing that Joan may have been suffering from the symptoms of Lyme Disease for months, a somewhat relieved Will and Helen believe this news may explain Joan's mood swings and atypical behavior, while a concerned Adam wonders if Joan will be different upon her recovery. Meanwhile, the hospitalized Joan experiences a crisis of faith -- and considers revealing to someone close to her that she's been talking to God. In separate circumstances, Helen and Will begin to rethink their belief systems after, respectively, experiencing spiritual dreams and miraculous events.

Joan baby-sits for a 6-year-old boy who is obsessed with death; officers assault a black man at a gas station.

After God tells Joan to give Adam a gift, she finds something that leads her to wonder if God's suggesting she have sex with him... While secretly searching through Adam's backpack for gift ideas, Joan is stunned to find a condom there. She soon wonders if sex is the ""gift"" God had in mind, and she nervously ponders whether or not she'd be ready for such a big step. Meanwhile, Kevin begins covering court proceedings for the paper and ends up causing a stir in one of Will's cases.

God tells Joan to join the debate team, where her partner has a stuttering problem. A new security system is implemented at Arcadia High School. After the art teacher quits, Helen wonders if she would be right for the job. Both Kevin and Luke seperately deal with the aftermath of a kiss. And Will and Toni deal with a case involving a reverend accussed of child molestation.

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.

Joan's newest mission from God is to work with kids, so she volunteers to help babysit children of abused mothers; Joan becomes jealous when Adam falls for one of the volunteers; Kevin starts to get cocky again and sleeps with his girlfriend, Rebecca; previous events emotionally catch up with Will; and Luke makes a shocking admission to Kevin.

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.

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.

16 year old Joan Girardi is approached by someone claiming to be God. He gives her a mission, get a job. Will Girardi, Joan's dad and new chief of police for Arcadia, is trying to solve the case of a serial killer.

God instructs Joan to help out with the a chaotic Girardi household; Adam has his first art show; Will and Toni witness a carjacking. Will and Toni, while making an arrest, get stuck in an elevator with a pregnant woman who is about to give birth; Kevin believes he might be recovering some sensation in his stomach area and gets an EMG (a nerve conduction) test done.

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.

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.

Joan learns from God that she's holding a garage sale on Saturday, which doesn't leave her much time to sort through her family's unwanted belongings. Among the items she unearths are paintings created by Helen during a dark period in her life. Elsewhere, Will goes to bat for a rape victim even though the district attorney feels the case isn't strong enough. Also, Joan catches the interest of a class charmer and a newspaper job falls right into Kevin's lap.

God tells Joan to do an extra credit English assignment on romance poets, which causes her to question her own love life.

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.

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 – 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.

Joan enrolls in advanced-placement chemistry, after God asks her to stop being an underachiever; Will ruffles feathers during an arson investigation.

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.

Helen fears Joan is becoming eccentric when she enthusiastically tackles her boat-building project; Will encourages Kevin to join a wheelchair basketball team.