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The son of Joseph McPhee, Jack is the shy new kid on the block when he and Andie begin their Sophomore year at Capeside High School. It is later revealed he and Andie had an older brother, Tim, who died prior to the series premiere. It is assumed Jack and Andie are fraternal twins, since they are both sophomores, beginning in Season two. Jack and Andie's mother, also named Andrea, is revealed to have a mental condition, something passed down to her only daughter.
At first, Jack is reluctant to become involved in the community, but soon befriends Joey Potter. Later, Jack offers Joey to pose in the nude as the subject of a portrait for her art class. The two begin dating, but their romance is quickly ended after rumors circulate about Jack's sexuality. This followed a cruel request by the gang's English teacher, Mr. Peterson, that Jack read a personal poem to the class. Embarrassed and ashamed, Jack fails to finish the poem during his first reading session, and is asked to relive the humility once more, at which time a brave and enraged Pacey comes to Jack's defense. While Mr. Peterson is ultimately shunned by the high school population and chooses to retire early, Jack remains under scrutiny about his sexual orientation. Jack later comes out of the closet and from then on is known as the 'Gay Guy.' Jack becomes good friends with Capeside's instigator, Jen Lindley, whom he convinces to move in with him after Grams kicks Jen out and he decides to remain in Capeside while his sister Andie seeks medical attention at a psychiatric hospital. Eventually, Jen moves back in with Grams on the condition Jack also moves in.
After his split from Joey, Jack realizes he has some issues of his own to deal with. When the group is invited to a party at a local golf course, Jack is reunited with his ex-girlfriend, Kate; the girl to whom he lost his virginity. Kate is still grieving after being dumped by her previous boyfriend, who confessed he was gay. At first Jack is to scared to tell her he also is gay, but after an overnight stay in prison for public drunkedness, he reveals to Kate he is gay. The two remain good friends.
Not feeling like he truly belongs in Capeside or any where for that matter, Jack finds comfort and friendship when he is convinced to join the Capeside football team by Mitch Leery, the new coach. Still coming to terms with his own sexuality, Jack attempts to have a fling with Ethan, a guy he met on the train on the way back from Boston and who he saw again at the store. Jack was invited to the annual Capefest which he attended with Jen, who he easily ditched for hopes of his first gay friendship experience with Ethan. His attempts to woo Ethan fail and Jack moves on to inspire a creative spark within Joey. However, Jack and Ethan are reunited for the gang's Junior Prom, organized by Dawson and held at his parents' restaurant, Leery's Fresh Fish. It is all just another plan orchestrated by Dawson to win Joey back. In the meantime, things don't go so well for Jack either. At the end of prom, Jack finds Ethan has left and chases him to the bus station where Ethan asks him to prove he is ready for a relationship. Jack cannot prove this though he is to afraid to kiss Ethan. Weeks later Jack finds himself on a crazy road trip with Grams, Jen, and Andie chasing after Henry, Jen's football playing boyfriend, so Jen can fix things before he is at football camp. While on the road Grams, Jen and Andie agree to make another stop at Ethan's boarding school so Jack can fix things. Jack rushes up to Ethan and kisses him, only to immediately find Ethan working things out with his ex-boyfriend, Brad.
At the beginning of the school year, Jack is looking forward to football most. It is his senior year and he is ready to be a leader on the team. But at the beginning of the season during a practice he lands wrong on his arm and dislocates it. Since he is unable to play football with a dislocated shoulder , Andie convinces Jack to help her coach a little league soccer team. But once Andie moves to Italy, Jen takes over her spot. He agrees and soon befriends Molly; a shy nine-year-old girl, whose much older sister, Caroline won't stop hitting on Jack. When he reveals to Caroline he's gay, the parents of his team go ballistic, threatening to fire him. But they are careful not to fire Jack 'because he's gay' (As it is illegal to fire someone on the basis of sexual orientation in Massachusetts.), but because he places Molly in as goalie after they ask him not to.
During the senior class ski trip, Jack and Jen almost sleep together after getting drunk, when Jen breaks into the liquor cabinet to get rid of her pain; she fell on ice and bruised her thigh. However, Jen quickly puts an end to their sexual encounter.
Jen finds herself getting into trouble with an old school mate and she is forced to do many hours of community service. She meets Toby, a gay activist, who she finds completely charming. Immediately she tries and sets Jack and him up but it fails. But Jen does not give up and somehow tricks Jack into going to his senior Prom with Toby. Following that night Jack and Toby embark on a happy relationship which doesn't end until season five when the distance and the changes they go through in college tear them apart.
Principal Peskin starts an investigation as to who put his sail boat, with his dog inside, in the school swimming pool. Peskin interrogates the three friends amongst others, such as class trouble-maker Drue Valentine, about the prank. It is only revealed later Jack, Pacey and Dawson did pull off the prank, although Drue was held responsible.
At the end of the season, Jack and Jen graduate from Capeside High with the Class of 2001. Joey and Andie are among the validectorians, and Joey is chosen to give a speech.
Before Jack is even a part of the fraternity he completely puts the fraternity before his boyfriend Tobey, Tobey, who refuses to be second to a bunch of drunken idiots, makes Jack choose. Of course Jack chooses the fraternity and then is found spending more time partying with his frat brothers and less time studying. As a result, he fails a few of his classes. When Jack learns he's failing out of school, he turns to alcohol in hopes of making the pain go away. When his frat brothers, particularly, Blossom, learn of his failure, they harass him during a group beerfest at Civilization. A drunken Jack retaliates, punching Blossom in the face and ends up cutting himself on a broken drinking glass. The next day, when Pacey tries to reason with him, Jack walks out. Jack is eventually kicked out of the fraternity because another frat brother tells everyone Jack came on to him when Eric actually came on to Jack. Towards the end during finals, Eric helps Jack get through them by using the Fraternity's information on what the tests are like.
During a spring break trip to Florida with the gang, Jen tries to confront Jack about his drinking problem. Jack jumps from the roof of the house, landing face first into the swimming pool. Dawson rescues him, and reassures him everything will turn out okay.
When everyone collides at the airport in the season finale, Jack is convinced to stay and work things out with his ex-frat brother, Eric, who has suddenly come out of the closet. Jen puts her plans for a trip to Costa Rica with Jack on hold to go visit her parents in New York.
At the start of his sophomore year at Boston Bay, Jack gets dumped by Eric via e-mail after spending a romantic summer with him. But he continues to experiment and date other men. Jack later moves out of Grams' house and in with Pacey and Emma Jones, an aspiring drummer who's dropped out of college. While at a Halloween party with the rest of his friends, Jack meets David, another student, who turns out to be gay, while Jack and Jen confuse him to be straight and his friend, C.J. to be gay. After Jack begins seeing David, he gets trapped in a crush-on-teacher situation when his feelings towards Professor Freeman, a married man, are reciprocated. This forbidden relationship has a direct effect on Jack's grades.
Things with Freeman quickly end when the professor leaves town without his wife, who had just lost the couple's child. Jack continues to pursue his fun relationship with David while Jen dives into a fling with C.J. Jack and David attend the No Doubt concert in Worcester, Massachusetts with Joey, Eddie, Jen, Audrey and Pacey.
During a party at the apartment he shares with Pacey and Emma, Jack participates in a game of Spin the Bottle. He ends up kissing Emma, Joey and Jen. In the meantime, Emma drops the bomb that she's engaged to an ill-mannered man named Gus. After revealing that she's only marrying Gus to avoid being sent home due to her Visa expiring and having to live with her mother, Jack 'proposes', since they already live together. Emma refuses, telling Jack that he's too good of a friend for her to marry in that type of situation.
While selling tickets to a Lovelines showing in the college auditorium, Jack meets Fred, another gay student who, at first seems interested in David. When Jack lets Fred sit where David should have been at the show, David loses it, accusing Jack of openly flirting with someone else. He announces to the entire auditorium that Jack was hitting on another student, but Jen tries to convince him that Jack was just being nice. Still believing that Jack is just in a relationship because he's out to prove himself, David demands an apology from Jack for the incident or else he'll break up with him. Jack apologizes, but David doesn't accept it; Jack is convinced that he's done nothing wrong. David and Jack eventually do split up for good.
Jen gathers Jack, C.J. and her mother at Grams' house so that she can tell them about her battle with breast cancer. When Grams' boyfriend, Bill Braxton (also C.J.'s uncle) burst in and breaks the news, everyone is shocked. Jen then decides that she and Grams should move to New York to live with her mother. They finally agree that moving is for the best and invite Jack to come along for the ride.
In 2008, Jack is an English teacher at Capeside High School. He and Pacey Witter's now admittedly gay brother, Doug Witter are in a relationship. Even six months in, Doug still seems embarrassed to be seen with Jack out in public. The two briefly separate due to the fact that Jack feels like he is being dragged back into a closet that is not even his but they are brought back together after learning that Jen Lindley, Jack's best friend, is dying due to a heart abnormality that did not show up until she became pregnant with her now 1-year-old daughter, Amy. She is afraid of dying, but most of all, of leaving Amy alone. During a break down, she asks Jack to make sure that Amy feels like she belongs. Jen confesses to Jack that she felt like she never really belonged. After listening to her confession, Jack tells Jen that she does belong, that she's always belonged to him and that they're soulmates. After her death Jack contemplates leaving Capeside to prevent Amy from having a repeat of his own childhood. Doug tells Jack that Amy will be the child of a gay parent no matter where she goes, and that "being a parent means knowing that your child is bound to fall down; you just have to show them how to get back up." Jack and Doug agree to give their relationship another try and to raise Amy together.
- Joey Potter: In season two Jack was Joey’s boyfriend for a brief period, creating tension in Joey and Dawson’s relationship. The two of them broke up when Jack came out of the closet.
- Ethan Brody: In season three Jack met Ethan Brody on a train heading to Capeside. Ethan was a student in a boarding school in Boston, but he had broken up with his boyfriend (one of his classmates) so he went to Capeside to spend some time with his family. Jack intended to take Ethan to his prom as his date but he wasn’t allowed to do that due the fact that they were both boys. In the season finale, Jack went to Boston looking for Ethan, just to realize that he had reconciled with his boyfriend.
- Toby: Jack met Toby in a gay support group in Capeside. At first Jack didn’t like him because he was “too gay”, but soon they became friends. Toby was Jack’s prom date in season four, and by the end of the season they had become boyfriends. Jack broke up with Toby at the beginning of season five.
- Eric: In season five Jack joined a fraternity; the other members of the fraternity supposedly didn’t have a problem with Jack’s sexuality, but Eric refused to be his roommate. Later, when Jack is expelled from the fraternity and needs to study for his finals, he gets help from Eric. Jack canceled his trip to Costa Rica in the last minute to stay in Boston and support Eric since he had just come out to his parents. Eric left Jack for a younger guy and broke up with him in an e-mail.
- Professor Freeman: At he beginning of season six Jack developed a crush on one of his teachers, Mr. Freeman. His feelings were corresponded, but Professor Freeman was married, so Jack didn’t pursue the relationship.
- David: Jack met David through C.J., who was Jen’s love interest at the time. They soon became friends and eventually boyfriends. David became jealous of Jack when he befriended other guy, accusing him of flirting with this guy, soon David broke up with him.
- Doug Witter: In the season finale, Jack and Doug were living in Capeside as domestic partners. Being a police officer in a small town, Doug didn’t want people to find out that he was gay, so he and Jack often pretended to not know each other when they were in public. By the end of the episode Doug had overcome his fear of coming out of the closet and offered to help Jack to raise Amy.
- Andie McPhee: Andie is Jack’s sister; they were very protective of each other in high school, since they were left alone to take care of their mentally ill mother. Andie was really supportive when Jack came out to his father.
- Joseph McPhee: he is Jack’s father, in the beginning he was a very distant father, supporting Jack and Andie only in an economical way. Mr. McPhee was very unsupportive when Jack came out to him, but by the end of season three he had accepted his son's sexuality and the two of them had become much more closer.
- Jen Lindley: Jen and Jack became best friends near the end of season two, when she was kicked out of her grandma’s house and Jack allowed her to live with him. Later the roles reverted when Jack moved in with Jen and her grandmother. Their friendship proved to be one of the strongest in the show. When Jen died in the series finale, it was Jack who took care of her daughter Amy.
- Evelyn Ryan (Grams): Jack moved to grams’ house in the end of season two; soon she became a substitute mother figure to him. Their relationship continued through the rest of the series.
- Pacey Witter: Jack and Pacey became good friends when Pacey defended Jack after a teacher forced him to read a poem that revealed his homosexuality. The two of them became roommates when they moved to Emma’s apartment in season six.
- Dawson Leery: In the beginning Jack and Dawson’s relationship was one of rivalry, since Jack became Joey’s boyfriend. After Jack came out of the closet, he and Dawson slowly became good friends.
- Amy Lindley: Amy is Jen’s daughter, and Jack is her godfather. When Jen died in the series finale Jack adopted Amy.
- Jack and Ethan’s kiss in the episode “True Love” was the first male gay kiss aired on network television.
- It is unknown if Jack is older or younger than his sister Andie, some even think that they are fraternal twins.