For the purpose of shortening this tutorial, it is assumed that your character has animations and is set up properly, with a T-pose animation and any other animations you want it to have.
This needs to be done first, to make it easier to add multiple animations to your character and to make it possible to reorient multiple animations in batches (see below).
If you select the character in the viewport, you'll see from the gizmo that it's facing in the negative Y-axis direction:
Negative Y-axis direction
This will need to change for the character to work properly in CRYENGINE.
To do this, click on the Reorient skinned character mesh (parts) button:
Reorient skinned character mesh (parts) button
This may take up to a few minutes.
We need a root bone, and a root bone is always created from the skin mesh. To create one, click on the body skin file in the Outliner:
Body skin file selected
A new bone will appear underneath your character:
New bone under character
And at the top of the hierarchy:
New bone at top of hierarchy
You can rename this if you want, the name does not have to be what the plugin assigns to it.
Create a skeleton .chr file by selecting the skin mesh (important, as after the previous step, the root bone will probably still be selected!) and clicking Create skeleton CHR from selected skin mesh.
Now that you have an origin file, you can easily add animations to it.
To translate the movement of the pelvis to the root motion so it can move along, under Extract Pelvis Motion assign the hipbone under From and the root bone under To:
Extracting pelvis motion
Click Extract Motion.
When the FBX Export window opens, make sure Animation is selected.
Because characters usually have more than one animation, the whole scene would need to be reset for every animation and you would even have to close and re-open the plugin. Because you made an origin file, simply reload that file and you can add your new animation to it.
If you have a large number of animations, there is a quick way to reorient all of them without having to go through the whole process for every single animation.
Under Extract Global motion to root node, select all directions if you want the camera to not follow the character root bone if the character is for example rolling on the ground.
At the moment of writing, there is a small bug in these options; the Forward (Y) and Sideward (X) directions are flipped, so if you want the camera to follow the character root bone when the character is moving forward, deselect Sideward (X).
Under Output Max Folder, select the Animations/Output folder you created earlier in step 3 and click OK.