"You're a really special girl, Jenny, and you deserve someone who's going to see that."
-Nate to Jenny (The Sixteen Year Old Virgin)
During the third season, Jenny continues to crush on Nate despite him dating her stepsister, Serena van der Woodsen. However, Nate is uninterested and rejects her advances. Consequently, Jenny sleeps with Nate's best friend, Chuck Bass before being banished from Manhattan by Blair Waldorf.
After breaking up with his girlfriend, Blair, Nate meets Jenny in Central Park and they begin a brief romantic relationship. In the short time they date, Nate buys her thong underwear and the two are accidentally filmed fooling around by Vanessa in a video that goes viral. However, Jenny takes the relationship more seriously than he does and he begins to back off when he sees how into him she is; namely after she paints his face in several art forms. He slowly stops talking to her and she realizes it's over when she sees him with Blair at a party he stood her up to attend.
In I Will Always Love You, Jenny and Nate reunite and she loses her virginity to him. This relationship lasts until she begins to pursue Blair's younger brother, Tyler Waldorf. At the end of the series, Nate leaves to sail around the world to avoid ruining Blair and Serena's friendship.
In The Handmaiden's Tale, Jenny attends the junior's only masked ball in disguise. At the end of the night, she trades masks and shrugs with Serena van der Woodsen and is grabbed by Nate, thinking she's Serena. He confesses that he loves her and wants to be with her before kissing her. Jenny pulls away and runs off right before the real Serena comes to tell Nate to look for Blair Waldorf. Realizing his mistake, he buys Jenny chocolates that he brings to school in the hopes of convincing her not to share what he did. She assures him she won't tell, as he's recently back together with Blair. Meanwhile, Blair's mother Eleanor Waldorf reveals that Nate's parents, Howard Archibald and Anne Archibald, were talking about how the van der Bilt family ring would eventually be Blair's. She takes this to mean that Nate is seriously planning for their future and gets so excited that she tells Jenny. However, Jenny knows that he isn't and tells Blair about what happened at the ball. Furious, Blair fires Jenny and she and Nate break up that evening after she explains that she knows what he did. In Seventeen Candles, Nate's mom, Anne Archibald, asks him to give Blair a special family heirloom in the hopes that it will ensure Eleanor's company loyalty in the wake of his father's arrest. However, Nate doesn't want to do so due to his break up with Blair. Outside her 17th birthday party, he runs into Jenny and they decide to take a walk instead of going inside. He reveals what his parents want him to do and she encourages him to make his own decisions.
Later, in A Thin Line Between Chuck and Nate, Jenny has her hopes dashed when Blair reminds her that they aren't friends. Meanwhile Blair, having recently slept with both Nate and his best friend, Chuck Bass, suspects she is pregnant. She asks Serena to buy a test for her and Serena is photographed on Gossip Girl buying it. When having dinner with Dan later, she confesses to him that she never thought she was pregnant but that Blair did even though she never told her directly that she slept with both Chuck and Nate. When Blair discovers she isn't pregnant, she rejects Chuck completely to focus on her new relationship with Nate. Angry at this, Chuck sends a tip to Gossip Girl that Blair slept with two guys in one week. When Nate sees the blast, he assumes it's false until a vengeful Jenny confirms the rumor. As a result, Nate breaks up with Blair, who eventually learns it was Jenny who told him. In the The Blair Bitch Project, Nate notices the change in Jenny's attitude after Blair is dethroned as queen and she's cemented as one of the girls of the steps. He warns her to be careful not to fall out of line with her new friends but she becomes defensive and says she won't. That evening, Jenny stresses over not having anything to wear to her birthday dinner with her friends but her prayers are answered when she stumbles into Hazel Williams' mother's closet, which is filled with designer clothes. She steals one and sells it to a consignment store in exchange for a $1200 Dolce & Gabbana dress. However, she later discovers that it was a specially designed Valentino that's worth $15,000. When she tries to trade the D&G with the store to get it back, the clerk informs her that it's not an equal trade. Having nowhere else to turn, Jenny calls Nate to borrow $8,000. Nate asks what she needs that much money for and she decides not to tell him. Concerned, Nate finds Jenny's brother, Dan Humphrey, and fills him in on her request. By the time he arrives home, Jenny's crime has been revealed to her friends and their father, Rufus Humphrey. Later that night, she sneaks over to Nate's to apologize and asks him to come with her to crash Blair's table at Butter. He agrees to go and Jenny gets her place back in the group.Chuck In Real Life, Dan discovers that Nate is living in the Archibald's home with no electricity or furniture due to the family's frozen assets. Wanting to help, he invites Nate to move in to the loft; an offer Nate eventually accepts. While living there he becomes closer friends with Jenny and develops a small crush on her, that he acts on in Pret-a-Poor-J after he finds her taking photos in her bra with her friend Agnes Andrews. Meanwhile, Jenny has recently quit working at Waldorf Designs and set out to start her own clothing line. Her first step is to find investors and she plans to crash an event at The Palace Hotel where many UES socialites will be and stage a guerrilla fashion show. When Nate discovers what she is doing, he agrees to support her and not stop her. After her show is a success, she kisses him but unbeknownst to the two, Vanessa Abrams, Dan's childhood friend who is interested in Nate, sees. At the same time, Dan kicks Nate out of the apartment for having a relationship with Jenny. Having nowhere else to go, Nate decides to go to the Hamptons to stay with his mother but mails a letter to Jenny confessing his feelings before leaving town. On Thanksgiving, Vanessa intercepts the letter before anyone sees it, including Jenny (The Magnificent Archibalds).
Having never seen the letter, Jenny believes Nate lost interest in her and moved on. However, she realizes this isn't the case when she sees a photo of him kissing Vanessa on Gossip Girl. Angry and jealous, Jenny teams up with Hazel, Penelope, and Isabel to humiliate her at the upcoming Snowflake Ball. She makes a dress for her with no lining that will reveal her underwear and bra in front of everyone and the plan works. Before the plan takes place, the guilt of stealing the letter convinces Vanessa to tell Nate she stole the letter and accept the consequences. Once Jenny's plan takes place, it ultimately backfires: Nate is disgusted by Jenny's viciousness and decides to pursue Vanessa instead. He tells Jenny about the letter himself, and says he isn't interested in her anymore after what she did (It's a Wonderful Lie).
After being sabotaged by Eric van der Woodsen, Nate steps in to escort Jenny during her debut at her Debutante Ball (They Shoot Humphreys, Don't They?). Meanwhile, Nate is struggling with his feelings for Serena and the two eventually enter into a relationship and Jenny has begun dating Damien Dalgaard, an old friend of Serena's. However, Damien wants to have sex with Jenny, but she is unsure about losing her virginity to him. When Serena discovers that she is planning on doing it, she plots with Nate to stop Jenny from doing so. This plan entails having Rufus crash Jenny's lunch with Nate to ground her, which works until he decides to attend an event to see Lily. He brings Jenny along and she has Damien meet her there. On their way out, Nate tries to stop them but Damien slows him by punching him in the face. Later that night, Jenny decides she isn't ready to have sex yet and Damien breaks up with her (The Sixteen Year Old Virgin).In The Empire Strikes Jack, Rufus attempts to get Jenny back on track by volunteering her to work at Eleanor's upcoming fashion show. Jenny is excited until she finds out Eleanor also hired back her old frenemy, Agnes, who is hellbent on getting revenge on her. At the show, Agnes drugs Jenny and leaves her at a bachelor party, which Nate witnesses her being taken to. He tracks her down to bring her home safely and this leads to Jenny realizing she still has feelings for him.
On Nate's birthday, Serena plans an extravagant surprise party for Nate but asks his friends to keep quiet and to downplay his birthday. Knowing almost everyone is ignoring him, Jenny uses this opportunity to spend some alone time with Nate and they go to lunch together. She also attempts to make him late for the party, which works for a time until they do arrive after a Gossip Girl alert is issued. The party entails a game of Assassin, where each player has a polaroid photo of themselves and is "killed" when another player successfully takes the photo. The game eventually ends up with Jenny and Nate as the final players and in order to win, Jenny kisses him. When Nate confronts her about the kiss, she says she used it as a distraction only but watches jealously as he and Serena later leave the party together (Inglourious Bassterds). Soon after, Blair's maid Dorota is set to marry her boyfriend, Vanya, in an impromptu wedding. The day of, Serena lies to Nate that she is having breakfast with her family when she is actually meeting Nate's enemy, Carter Baizen, who has information on her absent father. However, Carter later reveals this meeting to him in front of Jenny and Eric. At the wedding, Carter asks Serena to come outside and tells her that he has her father's current exact location in Palm Beach, Florida. She mulls this over briefly before deciding to leave with Carter and not telling Nate. On the way to the airport, she discovers that Carter has known where he was for weeks and didn't tell her in an attempt to woo her away from Nate. Angry, she kicks Carter out of the car and calls Nate's phone, which Jenny answers. Serena asks her to tell him that she's leaving but does't want any more secrets, and that she loves him. Jenny agrees to pass on the message but never does (The Unblairable Lightness of Being). As a result, Nate is angry that Serena is not talking to him and ends up spending more and more time with Jenny. When Serena eventually returns, Jenny is jealous that Nate is still willing to work it out with her. Meanwhile, Chuck is dealing with his break up with Blair and drunkenly tells Jenny that she actually has a shot with Nate now that Serena is back. To raise suspicion, she steals one of his shirts that she accidentally lets Serena see that she has. She confronts Nate about it and they start fighting about who is keeping secrets from who. That night, Nate agrees to go to a Brooklyn art party with Chuck and Jenny, but Serena gets upset when she realizes where he is. Later, he returns to The Empire with Jenny, who tells him how wonderful he is and that she would never treat him as bad as Serena does. When she realizes Serena has entered the room she tries to kiss him but he refuses. Serena confronts them both and reveals that she tried to call him at the wedding and that Jenny failed to pass on her message. Jenny tries to put the blame back on Serena but Nate tells her to get out. Offended, she does so.
Nate (to Jenny, thinking she's Serena): Serena, don't say anything just let me explain. I'm trying to do the right thing but it's killing me. Look, I know we both care about Blair but maybe the best thing is for me to just tell her the truth. I'm not over you. And I thought I could fight it but I can't. And if you don't stop me, I'm going to kiss you.
-The Handmaiden's Tale (1x06)
Nate (on doing what his parents want): I just think that, if I do this now, when does it ever stop?
Jenny: Well, it'll only stop when you stop it.
-Seventeen Candles (1x08)
Nate (to Jenny): You're a really special girl, Jenny, and you deserve someone who's going to see that.
-The Sixteen Year Old Virgin (3x15)
Jenny: Oh, God, waffles.
Nate: You don't like waffles?
Jenny: It's not a matter of like, it's-it's I'm a Humphrey so syrup is a food group.
Nate: Yeah, how are you not like five hundred pounds?
-Dr. Estrangeloved (3x19)