She finally opens up to Percy and explains the symbolism behind the beads and the college ring that she wears on her necklace during their ride in the zoo truck in chapter 16. The necklace is obviously very important to her. It symbolizes her memories, the people that are closest to her, as well as the trials along her own hero's journey.
In chapter 20, when Percy is about to battle Ares, Annabeth gives him the necklace:
"Wear this, at least. For luck."
She took off her necklace, with her five years' worth of camp beads and the ring from her father, and tied it around my neck.
"Reconciliation," she said. "Athena and Poseidon together."
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