Yet somehow the scientific method as we know it evolved in (and only in) Christian universities.

Of course there were significant regressions but the Roman world wasn’t exactly some pro-science utopia. Where do you think Christians got the idea of burning witches?

Climate change, the plague and extreme political instability (that already was ripping the Roman world apart for centuries) and the resulting societal, economic and demographic collapse pretty much made the dark ages inevitable (and the church was the only thing keeping the lights on however dim they were).