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.

God instructs Joan to ask a troublemaker to the winter formal. Will uncovers secrets that could prove unfavorable to the former Chief of Police and other members of the city's government.

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.

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.

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'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 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.

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.

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.

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.

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 – 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.

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.

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.