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Renee is suspicious when a friend's wife and other patients become comatose supposedly from allergic reactions to anesthesia. She suspects Sandoval when she sees hybrids at the hospital. She needs an Atavus blood sample to find an antidote.

A Jiridian probe headed for Earth is shot down by the Taelon Embassy and crashes outside of D.C. Liam recovers the probe, but he, Augur, and Julia are captured by another underground resistance movement led by the real Colonel Liam Kincaid.

Now that Adam has broken up with Iris to be with Joan, she's worried that they don't have enough in common for their relationship to last. God suggests she join the yearbook and she thinks that photography might be her artistic link to Adam. When Joan's photos aren't very good, her mom stands up for her but is accused of playing favorites. Trying to still be helpful, Joan throws away poems that were intended for the yearbook and has to go dumpster diving to find them. Friedman misses spending time with Luke, who is occupied with girlfriend Glynis, so he begins to boast about a girlfriend of his own.

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 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 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 over again.

Joan is struggling with math when God tells her to take some piano lessons. She agrees to do some cleaning for the cranky piano teacher in exchange for some lessons. While looking for her old piano books, Joan finds some pictures of her dad and a letter that mentions Richard. When she asks her parents about him, they tell her to forget about him, but she asks Luke to investigate. Kevin will not give up hope about neural regeneration even though the doctor says it is unlikely.

Joan is bummed that Adam has Iris and Luke has Glynis and she's alone. God tells her to join in jumping rope with a group of girls in the park. After some difficulty, Joan gains their respect and befriends Casper, who is homeless. Joan tries to help her, but it backfires. It's bring your kid to work day and Will takes Luke along, but since he's relegated to desk work, he sends Luke with the CSI lab guy, but Luke would have rather spent the time with his dad. An author that Kevin interviews hits on him and he just can't resist.

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.

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.

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.

Kevin seems back to his old self, participating in the wheelchair basketball games and picking on Luke, but Luke is fed up with the whole jock vs. nerd scenario and they have a fight. Meanwhile, things are heating up between Kevin and Rebecca. God ruins Joan's plan to go to a concert with Adam when she is tasked with doing art therapy with kids on the same night. He takes Iris instead, which makes Joan jealous. Will is put on psych leave after pulling his gun on a child during an investigation.

After a picture of Joan wearing only underwear in the locker room is leaked throughout the school, her friends plot revenge for her. But sometimes, revenge doesn't work out the way you hope. Things also go awry when she tries to help out by doing laundry at home. Will investigates the case of an older man who drove into a marketplace and killed 6 people, including a child.

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.

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 for emotional damages.

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 testify, which turns out to be justified.

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 them win their court case.

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 is still struggling with Adam and Iris being together, but she agrees to help him set up his art at a coffee shop. Luke is sick at home and Joan tries to help her mom out by checking on him and cooking dinner. When he realizes he needs something in his notebook that Grace has, Joan goes on a hunt for it. She is having trouble meeting all her responsibilities and feels guilty about failing at handling adult tasks. Kevin believes he has feeling where he hasn't since the accident and is hopeful that he is experiencing neural regeneration. Meanwhile, Will is stuck in an elevator with an embezzler and a woman who gives birth.

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 her 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 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.

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.

Helen has a strange dream, partly reliving the night of Kevin's accident, and also including a conversation with God about Joan. On the last day of school, Joan has a rash on her leg and isn't feeling well. Rumors have spread about Joan and Adam being at the hotel together and she has to keep denying that they had sex. When she collapses and is taken to the hospital, the doctor has a diagnosis that may explain away her visions of God as hallucinations. Meanwhile, Will deals with a hostage situation and the aftermath. Helen is at the church when she has a bad feeling and senses something is wrong with Joan.

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. Kevin's relationship with Lilly is threatened when she reveals that she is thinking about returning to her former profession.

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.