Serena Van der Woodsen is a runner, plain and simple. When the going gets tough, she gets going.
When Serena was fourteen, her mother caught her smoking up with a boy on the water polo team. Serena took a taxi to her grandmothers and didn't come back for a week. This should have been a sign.
It shouldn't have been a surprise to anyone when she ran away to boarding school. It also shouldn't have been a surprise when everyone found out she slept with Nate, he was hers to begin with.
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Nathanial Archibald is a watcher, past and present. While everyone is moving, he stands there letting it happen.
When Nate was fourteen, Lily Van der Woodsen caught him, the boy on the water polo team, smoking out Serena. He stood there while she screamed. He continued to stand there while Serena ran away. Nate saw the signs.
When Nathanial and Serena had sex, he was just following her lead. Not to say that he didn't want to have sex with her, because Lord knows he did, that hair, the legs, those lips. Nate wasn't surprised when she ran. He was surprised, however, by how much it hurt.
He figures it's time he stops watching and starts acting.