Active Sites versus All Sites
Netcraft reports both "active sites" and "all sites". "Active sites" represents domains with real web sites behind them. "All sites" is mainly just domain names that are owned by speculators or domain squatters with no real web site other than a "this domain for sale" site or link farms. A real web site requires real infrastructure to support it, while a single server can support thousands of inactive ones (they rarely if get visited, except when someone makes a mistake typing in a domain name).
In other words, the "all sites" statistic is meaningless. However that's the only one where Microsoft has a significant market share. When it comes to active sites (that is real web sites), IIS has been in third place for quite a while, after losing second place to Nginx. There will be month to month statistical variation, but the long term trend for IIS has been inexorably downwards for many years. They had a bump a few years ago which turned out to be domain squatters and link farms temporarily showing up as active sites until Netcraft filtered them out again. Netcraft used to publish much more detailed statistics which showed this, but their newest reports are less informative.
Netcraft also tracks the top million web sites in terms of traffic. Those have always mirrored the "active sites" numbers pretty closely (minus the domain squatter bump). In other words, the anomaly is the "all sites" figures. Apache hasn't "returned". When it comes to real web sites, Apache never left.
The only real news over the past 5 years or so has been the rise of Nginx. That has been popular lately due to it being easier to configure. Since it simply doesn't support the more complex use cases that Apache does, it has fewer knobs to twiddle.
The differences between Netcrafts "all sites" and "active sites" has been well known in the industry for years. If you still see a report today that confuses the two, you need to take anything else in that report with a very large grain of salt.