What is the nucleophilic atom in the Williamson ether synthesis?

The Williamson ether synthesis is a standard SN2 mechanism reaction. That being said, just think about it.  A primary alcohol becomes an alkoxide ion and reacts with an alkyl halide to form an ether.  Since alkyl halides, and most halides (Cl- and Br-) make great leaving groups, the alkoxide acts as the nucleophile.

An example using ethanol and methyl bromide (alkyl chlorides are kinda pesky, and often need a catalyst):

2 H3C-CH2-OH + 2Na 2 H3C-CH2-O-Na+ + H2(g). (formation of the alkoxide ion)
H3C-CH2-O-Na+ + CH3-Br -> H3C-CH2-O---CH3---Br (the transition product, according to SN2) -> H3C-CH2-O-CH3 + Br-

Hope this makes sense.