To most modern medievalists this period is no longer known as the Dark Ages, but the early middle ages, which usually is defined roughly from 300-1000 but some historians will differ in their range. However, there are a lot of stereotypes surrounding the early middle ages that recent research has forcefully responded to (although a lot of this is yet to catch on to the mainstream).

First, that the dark ages were some sort of primitive time after the fall of Rome in 476 that plunged western Europe into a period of chaos and anarchy. In many ways this is a faulty interpretation which was first proposed during the Renaissance. After 476 there was still a lot of continuity between the former empire and the successor states, be it in terms of the Gallo-Roman aristocracy and state structure of tax collecting (at least for a while) to later kings and emperor's purposefully resurrecting and reusing Roman ideas/tropes/etc. A good book that has dealt with this is Ian Wood's The Merovingian Kingdoms where he discusses the survival of aristocrats after 476 but also the continuing of the Roman letter writing tradition in Gaul. Another good source (although you likely need a pretty substantial library to access it) would be the Transformation of the Roman World series, which has several of volumes dedicated to the subject. In the centuries following 476 there were no 'centralized' powers in the sense that Rome was, but I would argue that centralization does not necessarily indicate an advanced polity. Finally, a lot of arguments have been advanced that the early middle ages were characterized by predominantly oral societies which relied on the written word less than the Romans did. From the 8th century onwards this has been shown to be pretty much false, with the written word being a huge part of society. The work of Rosamond McKitterick was hugely influential here, but more recent works have expanded on the subject, especially documentary culture amongst the laity. Sources bring me to my second point.

Second, that the dark ages are dark because there is little evidence surviving. However, this may only be an issue for the 6th to mid 8th centuries. Even then, we do still have a pretty large amount of evidence to work with, its just not as much as later historians have access to. With better analysis historians have been able to extract a huge amount of information from these documents, as well as archaeological evidence.

Now, with all of that out of the way, some of your questions I can answer! In terms of which area was affected the most, it would depend on how you define it. If the loss of Rome was the key factor, then probably the areas north of the Alps that were formerly Roman, as opposed to areas further afield which were not formerly part of the empire. For them things would not have been impacted as much by the end of the empire. However, even within the former empire things did not collapse overnight, it was a gradual process. Obviously some stuff that was exclusive to the empire would have ended but in many instances things continued to function.

Disease was a concern at this time period, and there were a few big plagues in the 6th century, which you can find explored in a lot of detail in Michael McCormick's book The Origins of the European Economy where he talks about the transmission of a widescale plague across the Mediterranean. Further later in the 9th century there are a few more localized outbreaks of disease which proved quite deadly, in one instance killing off a large number of nobles.

I hope this was helpful, if you have any other questions do let me know!