  Extremely large opaque troughs in the Lyman-alpha forest have been
interpreted as a sign of an extended reionization process below z~6. Such
features are impossible to reproduce with simple models of the intergalactic
ionizing background that assume a uniform mean free path of ionizing photons.
We build a self-consistent model of the ionizing background that includes
fluctuations in the mean free path due to the varying strength of the ionizing
background and large-scale density field. The dominant effect is the
suppression of the ionizing background in large-scale voids due to
"self-shielding" by an enhanced number of optically thick absorbers. Our model
results in a distribution of 50 Mpc/h Lyman-alpha forest effective optical
depths that significantly improves agreement with the observations at z~5.6.
Extrapolation to z~5.4 and z~5.8 appears promising, but matching the mean
background evolution requires evolution in the absorber population beyond the
scope of the present model. We also demonstrate the need for extremely large
volumes (>400 Mpc on a side) to accurately determine the incidence of rare
large-scale features in the Lyman-alpha forest.
