  Using a self-consistent atmosphere code, we construct a new model of the
atmosphere of the transiting extrasolar giant planet HD 209458b to investigate
the disparity between the observed strength of the sodium absorption feature at
589 nm and the predictions of previous models. For the atmospheric
temperature-pressure profile we derive, silicate and iron clouds reside at a
pressure of several mbar in the planet's atmosphere. These clouds have
significant vertical extent and optical depth due to our slant viewing geometry
and lead to increased absorption in bands directly adjacent to the sodium line
core. Using a non-LTE sodium ionization model that includes photoionization by
stellar UV flux, collisional processes with H_2, and radiative recombination,
we show that the ionization depth in the planet's atmosphere reaches ~1/2 mbar
at the day/night terminator. Ionization leads to a slight weakening of the
sodium feature. We present our baseline model, including ionization and clouds,
which falls near the observational error bars. The sensitivity of our
conclusions to the derived atmospheric temperature-pressure profile is
discussed.
