It all really depends on how the device operates the system.
Others here are telling you to tap the interface, and try to emulate it.
As another approach, take a look at the at the program that is used to control the device.
The trick here is instead of decoding some protocol between the computer and the device, instead, tap in to the computer to drive the program that drives the device.
A potential tact for this is to install a TSR (Terminate and Stay Resident). The TSR does several things.
One, it intercepts the keyboard interrupts within DOS, and is thus able to "send commands" to the program. If "turning the fan on" entails going through a couple of menu options, then you can simply mimic the keyboard strokes necessary to navigate the menus, select the fan, and "turn it on".
For example, say if you hit ESC 5 time from anywhere, you get back to the main menu. Then, to get to the fan controller, you go to "Menu 2" which brings up a form listing the fans. You want "Fan 2", and when you arrow down, and hit enter, you get to a form that has a "Fan Status" box with a "ON" "OFF" toggle, which you can TAB to and then hit F2 (yes, I'm making this all up).
So, send it ESC-ESC-ESC-ESC-ESC (gets to main menu from anywhere), 2 (Menu 2), Arrow Down (Fan 2), ENTER (fan screen), TAB (to the field) F2 (toggle).
Two, it can monitor the screen that's shown by the program and then "screen scrape" it to deliver output to your controller.
Third, it can install a serial interrupt handler (assuming one is available) that can be used by you to send and receive commands from your controller to the PC.
If the serial port is unavailable, the printer port might be open -- you can use that too.
You may also be able to install an Network card and a TCP stack (or NetBios, to something else).
If it's running a version of Windows (pretty much any version), it can be even easier as you can tap in to the event stream for the program, and simply send it messages -- mouse clicks, keyboard events, etc. Screen scraping is a little more difficult, but you can even read the values of controls (like text boxes and labels) on the Windows forms from a separate program. Reading the temperature from a bar chart graph is left as an exercise for the reader.
Your controller can be something like a Raspberry Pi, with Wifi. It can present a simple web interface, and interact with the PC via the Serial port and the TSR. The DOS machine will, likely, "never know what hit it" or even know you're there.
All that said, "it's a hack" to be sure. But possible. It may or may not consume a bunch of time, lots of unknowns.