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.

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.

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.

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.

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 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.

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.

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.

After Joan stands up for one of her classmates being bullied, an embarrassing picture of Joan, taken with a picture phone, is rapidly spread around school. God instructs Joan to join the band. Will must deal with an elderly driver who accidentally killed several people.

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.

God's mysterious ways once again bewilder Joan, when He asks her to volunteer at the high-school art show, so that she can keep Adam Rove's sculpture from being exhibited. Elsewhere, Will feels pressure from the DA's office to call a man a hero after he shoots and kills a home intruder. Meanwhile, Kevin grows weary of receiving special treatment because he uses a wheelchair.

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.

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.

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.

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

God encourages Joan to learn how to play chess; Will must work with a psychic on a missing toddler case; Helen hopes a miracle will enable Kevin to walk again.

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

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.

At Helen's insistance, she and Will take a getaway to a spa, but all does not go well when Will cannot forget about his job. And with the parents away, the kids are up to a little recreation of their own; Kevin and his boss, Rebecca, find it hard to ignore their mutual attraction; Joan, as she is trying to sort out her feelings for Adam, is instructed by God to throw a party while her parents are way; Luke helps Joan pull off a successful party.

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.

Joan takes a cosmetics class, per God's request, and Kevin doesn't react well to crossing paths with the last girlfriend he dated before his disabling accident... Glynis' flattering makeover attracts a great deal of positive attention at school, which only adds to Joan's disappointment when Adam fails to notice her own new look. Meanwhile, Kevin, who remains bitter with the belief that he had been dumped by Beth because he had become a paraplegic, harshly rebuffs her efforts to make peace with him.

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.

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.

God tells Joan to take piano lessons; Joan helps her piano teacher deal with her past; Joan learns a painful secret Will and Helen have been keeping from the family; Iris becomes suspicious of Adam and Joan closeness.