The Sloan Digital Sky Survey, data release 5 (DR5), provides over 10,000 high redshift quasar spectra, such that the Lyman alpha forest can be seen. This dataset provides an unprecedented statistical view of the cosmological distribution of hydrogen and yields the surprising discovery of an apparently abrupt change in the cosmological hydrogen opacity evolution at a redshift of 3. I will present brief details of the analysis of this large dataset and discuss the cosmological information that can be extracted from it, noting particularly the re-ionization of HeII as the most likely explanation for the signal detected. If this interpretation is correct, this is the first ever re-ionization detection.