We do not know. One theory is that it was due to a mutation of the flu making it more deadly. It is also possible that the reporting on the number of dead was wrong. First wave hit when soldiers were moving to the front and nobody knew about the flu, second wave hit when soldiers were going home and everyone were looking out for the flu. A soldier dying in the trenches from an unknown illness is likely not going to be counted the same as a soldier dying from an illness on the way home in the middle of a known widespread pandemic.
The 1918 flu pandemic not only happened in the middle of a world war but also in the early development of our understanding of infectious diseases. We did not have to tools and techniques to study and track the flu like we do today so there is a lot of things we do not know about it. And the techniques used to combat the current pandemic is techniques that were developed during the 1918 flu pandemic. Restrictions such as limiting the number of people together, canceling public events, closing boarders or at least quarantine people who travel, regularly washing of hands and face, stopping the exchange of spit, etc. were all implemented during the 1918 flu pandemic and were shown to be highly effective. And then just as now the cities that did not take effective measures early had field hospitals overflowing with sick, morgues running out of space and people buried in mass graves.
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