As a simple example, when Windows started up, it increased the size of MS-DOS’s internal file table (the SFT, that’s the table that was created by the FILES= line in config.sys). It did that to allow more than 20 files to be opened on the windows system (a highly desirable goal for a multi-tasking operating system). But it did that by using an undocumented API call, which returned a pointer to a set of “interesting” pointers in MS-DOS. It then indexed a known offset relative to that pointer, and replaced the value of the master SFT table with its own version of the SFT. When I was working on MS-DOS 4.0, we needed to support Windows. Well, it was relatively easy to guarantee that our SFT was at the location that Windows was expecting. But the problem was that the MS-DOS 4.0 SFT was 2 bytes larger than the MS-DOS 3.1 SFT. In order to get Windows to work, I had to change the DOS loader to detect when win.com was being loaded, and if it was being loaded, I looked at the code at an offset relative to the base code segment, and if it was a “MOV” instruction, and the amount being moved was the old size of the SFT, I patched the instruction in memory to reflect the new size of the SFT! Yup, MS-DOS 4.0 patched the running windows binary to make sure Windows would still continue to work.
And these are the people who design and implement most widely used software in the world. Which is a scary place indeed.