They would be assessed at a civilian facility, one that had a mental health in-patient capability. Depending on how disorganized they were or what their state was, you may need one of the locked facilities, and there are not many of those. The attending civilian psychiatrist would institute immediate treatment. At the point where they had settled down somewhat, then care would be transferred to the mental health clinic in Valcartier.
Now, as to the chain of command's role, they of course are keeping track of what's happening, and they are thinking about what adjustments they have to make to the immediate pre-deployment training plans. It's not a tough decision to say this person shouldn't go on the rotation. That's the easy part. And then what?