The 96 fps on the 6d is done with a customized crop_rec module.
I promised to upload that build a long time ago

Ok, now I'm going to upload it

I've waited that long because it is not very stable and is not reliable and it probably works best with settings I'll give now

You're probably want to have experience with magic lantern and raw video and a little knowledge about post production and be able to unstretch the footage to the right aspect ratio. (it's recorded with 4 x lineskipping, just as Canon does in 720p mode, so footage needs to be vertical stretched with a factor of 1.67)
1440 x 354 resolution, which is recorded, will give you a unstretched resolution of 1440 x (354x1.67)= 591 pixels, almost about 1:2.4 ratio.
Some instructions:
Turn on the camera in video mode and use the menu button to enter canon menu, now change movie rec.size to 1280-50fps all-i. (it's in the 6th tab)
The above can be done without ML and even without SD card in your camera, it's just setting your camera in 1280x720 x 50fps video mode.
(If trying to use this setting in normal 1080p mode, you're camera will soft brick, it doesn't respond to the on/off switch and you must pull out the battery and put it back in to get life back in your camera

)
Download this crop_rec module for 6d (Not for the faint hearted

)
https://drive.google.com/file/d/1MalTVtGvQfoKsTPtV9oC7YQ7J811tvDw/view?usp=sharingPut it on your SD card in the ML/Modules/ folder.
Turn on your camera and enable the crop_rec module on the module tab.
Turn off and on your camera so the module will be loaded during startup, this gives a new option 'crop mode' in the movie tab, within ML menu.
Before activating the crop mode, I advise to go into raw video menu and set your preview option to 'frozen LV'.
I've just tested it, and it seems to work most reliable with frozen LV. (With other settings I got very often a top display 'error 70' camera shutdown

)
Now that's all set enter ML menu and in the movie tab go to crop mode and select 1440 x 354 100 fps option, jup that's right, this is the special 100 fps edition instead of 96 fps

Now the crop mode is selected, turn of your camera, set the switch to video mode (works best if your camera starts up directly in video mode)
and switch the camera on.
You will see a 50 fps normal live view.
Hold down half shutter press and you will see the ML preview, right.
Now let go with the half shutter press and use the magnify button and cycle trough the different modes(1x,5x and 10x) until you're back in normal view, so the magnify button needs to be pressed 4 times.
Now try the half shutter preview again, most of the times it works and now you will see the framing preview of what will be recorded in 100fps.
If the preview looks broken, which happens sometimes, cycle through all the zoom modes again with the magnify button, and try half shutter press again in normal view mode.
Once your half shutter press preview works, you can frame your shot, let go the half shutter press and hit the start/stop button to start recording.
you will probably see a black and white low resolution ML preview, refresh rate of the screen is slow, the whole camera and menu responses a little slow when this crop mode is enabled...
If you're unlucky, your camera shutsdown during recording with 'error 70' displayed on top display. But no worries, turn your camera on and off again and it should work. If not, pull out battery and put it back in and turn on the camera, everything should work. I've had a lot of crashes during testing and never destroyed my camera. Sometimes when a battery pull is needed, the refresh rate of my liveview looks a little messed up, flickering. But after a few minutes of camera usage and turning it on and off a few times, things got normal again.
So this specific crop rec module is not for the faint hearted
For anybody who is interested in the source, here it is:
https://drive.google.com/file/d/1c-Z0s5qqv40me1PSTf2KQ4nr-y4X-g2u/view?usp=sharing