It is questionable if one can call something like a virus or bacterium a 'villain', but assuming one can do this, there are several real-life examples of this trope among them.
It is a frequent (though not a universal) observation that a pathogen that has newly crossed the species barrier into a new host (say, humans) and is now capable of spreading in that new host for the first time will cause rather severe disease. (That's the initial 'scary villain'.) However, after a couple of epidemics the pathogen adapts more and more to its new host and often becomes less pathogenic in that process, 'decaying' into a comparitively harmless phenomenon. (To be precise, increasing immunity of hosts plays a role here as well, as does the selection pressure the pathogen exerts on its host.)
A good example of this is the measles virus which is rarely fatal (like ~0.1% death rate) in western civilizations where it has been circulating for centuries, but which proved devastating to indigenous people elsewhere who got in contact with it for the first time (death rates 10 to >50%). Today, indigenous people whose ancestors have been dealing with it since two or more centuries also aren't affected as severely any more.
There is also a theory that the flu pandemic of 1890 was actually caused by the coronavirus HCoV-O43 and not an influenza virus, while today HCoV-O43 rarely causes more than a cold. It was an outsider theory initially but got more known during the current Coronavirus pandemic, and if there is something to that theory it gives hope that Sars-CoV-2 will undergo a similar 'villain decay' in the future.
HIV/AIDS is also expected to become less deadly over time, but that is expected to take a little more time...
Not to say, there are some exceptions or "aversions". For example, the Variola Major strain of smallpox virus apparently has been deadly all the time from ancient times until its erradication in the 1970s.
As said, if one can call microbes 'villains'...