Not sure if this counts as an ad, but this has happened 2-3 times for me already. I thought it was just something I picked up on another website and reset Chrome, but it occurred again on this site.
Page(can be seen in screenshot 000.jpg): http://vatoto.com/read/_/183803/gakkou-gurashi_v1_ch6_by_norway-scan/9
OS/Browser: Windows 7, Chrome
Seems like Fake malware popup, not really an ad.
The popup appears under the address bar and prevents scrolling on the page. It seems like the popup also has the address of the page that is calling it, which can be seen in the screenshot.
After struggling a bit with the popup, it appears that the ad right above the comic image was also replaced with something similar to the popup. Chrome tab also indicated that the page was playing a sound.
Clicking ok removes the ad for roughly 2 seconds before it pops up again. Attempting to navigate away from the page in that time asks for confirmation to leave the page. There is also an option to "prevent further pop-ups on this page" which may just be a Chrome option.
Edit:
Happened again on http://vatoto.com/read/_/220147/gakkou-gurashi_v4_ch20_by_deeltl/18
Seen in images 001.jpg and 002.jpg
This time I also took a screenshot of the ad that I think caused it. It has a blue screen of death sort of color and a scroll bar. Looks like the text also mimics what you might see when you get a blue screen of death. It also plays sound.
Edit 2:
This "ad" may just be malware on my computer.
With the help of Google-fu, I found this: http://malwaretips.com/blogs/remove-tech-support-scam-popups/
so it may just be something I picked up on my own, and not part of this site. However, I don't think it explains why an ad on this site would change as well.
Edited by Seiris21, 22 October 2015 - 09:16 PM.