"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)
Jenny and Nate date in Season 2 for a brief time. They are secretive at first because Jenny is worried Vanessa - who is like a sister to her - will find out about their relationship. However, when they kiss and Vanessa sees, Jenny runs away from Nate effectively ending the relationship. She sabotages Vanessa causing Nate to realise that Jenny will always be two years younger than him and nothing he ever does will change that, however Nate still cares deeply about Jenny. He chooses Serena over her though and this is one of the key reasons that Jenny sleeps with Chuck and gets banished in the first place.
In the novels, Jenny and Nate date only when Nate isn't with Blair. Jenny and Nate 'fool around' in Sheep's Meadow while Vanessa films them. After this fiasco, the two don't reunite until the final book, in which Nate goes to a party with Jenny rather than Blair or Serena. In I Will Always Love You, Jenny eventually reunites with and loses her virginity to Nate, and they date seriously for a while until Jenny pursues Blair's younger brother, Tyler Waldorf. At the end of the series, Nate tries to confess his love for either Blair or Serena.
In Season 1 Jenny and Nate are purely platonic, he looks out for her when she becomes involved with the mean girls and thinks of her as a little sister. When she asks to borrow money, he informs Dan to make sure Jenny is okay, and she tells him the truth about Blair sleeping with Chuck first.
Season 2EditWhile his family's assets are frozen due to Nate's fathers impending trial, he moves in with the Humphrey's for awhile. While living there, him and develop a mutual crush on each other but don't know how to navigate it. Due to Nate and Vanessa's history, Jenny is unsure because of her long friendship with Vanessa and doesn't want to hurt her. After Nate crashes Jenny's inappropriate photoshoot with Agnes, the two share a passionate kiss. Unbenownst to Dan, who hates the idea of his friend dating his younger sister, Nate and Jenny continue their clandestine relationship. During Jenny's surprise fashion show at an event honoring Lily and Bart Bass, the two kiss and Vanessa sees, and leaves. Jenny, realizing that her worst fear has come true, runs after Vanessa and tries to smooth things over with her friend.
Meanwhile, a distraught Nate sends Jenny an apologetic letter confirming his feelings for her and his frustration over how to continue their relationship. However, a jealous Vanessa is able to intercept the letter before it reaches Jenny, effectively keeping Jenny in the dark about Nate's feelings for her.
Later, having never seen the letter, Jenny believes Nate just blew her off and was not interested. But when she sees a photo of Vanessa and Nate kissing on Gossip Girl, Jenny decides to gravely humiliate Vanessa. 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.
In Season 3, Nate is constantly looking out for Jenny, protective of her, and saving her from whatever trouble she gets herself into. Jenny and Nate dance together at the ball when Eric and Blair's sabotage at Cotillion fails. Jenny still likes Nate and spends lots of the series attempting to break Serena and Nate up so she can be with him instead. In The Empire Strikes Jack, Agnes drugs Jenny and Nate picks her up from the bar where Agnes and her model friends left her. Jenny uses this to pull Nate back in at times. They spend the beginning of his birthday together, and they seem to be happy and playful together. Jenny's plan doesn't work and when she kisses Nate, he realizes her plan from the start, he tells her that he wants to be with Serena. When Serena leaves Dorota and Vanya's wedding with Carter Baizen to find her father, she tries to call Nate to explain but Jenny answers instead. She tells Serena she'll pass her message along to Nate but never does, and instead just tells him she left with Carter. However, when Nate and Serena find out what she did, they both ask her to stay out of their relationship. Jenny is especially humiliated when Serena gets mad at her, she sleeps with Chuck and is the one who takes the photo of Serena and Dan in bed together. Once she sends this to Gossip Girl she knows it will break up Serena and Nate, but because of her being banished she still isn't with him.
Jenny: "Please, Nate, please don't go. I really need you here."
Jenny: "I'm a Humphrey; so syrup is a food group."
Nate: "How are you not five hundred pounds?"
Jenny: "What's wrong with me?"
Nate: "Nothing's wrong with you."
Jenny: "So, why do you care so much?"
Nate: "You're a really special girl, Jenny, and you deserve someone who's going to see that. You know, like someone who's gonna be there in the morning?"
Jenny: "It's not like you're available."
Jenny: "Did I mention public embarrassment is part of the Humphrey birthday tradition?"
Nate: (Chuckles) "I think I'm actually glad to be humiliated."
Jenny: "Good. Now blow out your candle and make a wish."
Nate: (Grunts playfully and blows out candle).
Jenny: (Laughs and claps) "Yay!"
"It's just whenever I'm alone I can't not think of the other night, you know? It's just, you're the only one who gets what I'm going through."
- Jenny to Nate.
Jenny: "Gee, thanks. As if it wasn't embarrassing enough when you fell asleep in the middle of my sentence."
Nate: "What, you mean monologue?"
Jenny: "You kissed me."
Nate: "I know."
"That guy is totally into you."
-Agnes to Jenny about Nate
Nate: "...I'm coming to get you."
Jenny: "So, thanks for saving me again."
-Jenny to Nate