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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.
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.
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.
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.