As I've mentioned before, the sudden cut back to 16-bits is supposed to indicate that the comic has broken out of the recreation and the events depicted are supposed to be "really" happening. I'm not sure what meaning that has in a comic strip, though.
After having Dr. Wily break out of the recreation and escape in the previous comic, I decided I wanted him to do something really evil, really over the top. But then I had to stop and wonder what that would be. What would be the worst thing he could possibly do? How about capturing the Author, effectively the god of the comic? Yeah, that'd do.
Now, if you've already read through the comic, then you would know that these events are directly related to the end of the comic. Of course, I didn't know that at the time. If there's one thing you'll learn about me while reading this commentary, it's that I almost never plan things out that much. There's some planning, but not that much. And if you haven't read through the comic before, then you'll almost certainly forget what I've just said by the time you get to the end of the comic.
By the way, I think this is the first time in the comic someone has uttered the phrase, "This is bad, right?" It's one of my favorite lines.