Well MC's is currently under a dillema.
On one side there is this system, that helps him to keep his cool under any situation, klling his emotions, instantly making him have calm decisions based on the events occuring.
On the other side, if MC ego is killed by the system, who is MC. What separates him from the system? If his conclusions are there thanks to the system(skill), isn't it possible that all "his" conclusions, are from the system and not his?
What defines a being as being himself and not any other, isn't that the ego? That is being bent by the system. So MC himself is being bent by the system.
Thus we have the mental breakdown, which is MC ego trying to resist the effects of this skill.