At yet another crisis in the relationship, Caroline found an apartment for herself in the 9th arrondissement and moved there on 5 August 1842.

This time the separation proved final.

She left Comte just after the completion of his Cours de philosophie positive.

Caroline recognized that the problems with the marriage were due to her insistence on equality.
She wrote,
I have always been devoted to you, but I was not at all submissive.
If there had been less real devotion and more submission, things would have been better between us.
Many times you were basically right, but you asked me to yield in the name of your authority, and I stood up to you when I should have submitted.
Really, I did not know how to be submissive, but even so, I did love you.
You know that very well. ...
My great crime was to see in you a husband, not a master.
I know very well that you are superior to me in many respects, and besides, this comparison has always seemed to me . . .
most absurd.
We did not do the same things.

Comte wrote to John Stuart Mill on 24 August 1842 to pour out his troubles,
Our personal friendship (...) causes me not to wait any longer to give you an important piece of personal news.
A fundamental change, more favorable than unfavorable, has occurred in my household since my last letter.
Madame Comte has left me voluntarily and probably irrevocably.
For seventeen years I have been married, as a result of an unfortunate love to a woman of rare moral and intellectual qualities, but brought up under blameworthy principles and with a false notion of the essential function that her sex must play in the human economy.
Her total lack of affection for me has never made it possible for me to overlook either her resistance to my authority or her despotic character.
There have been none of the compensations of a loving disposition, the only special quality in which women are irreplaceable, and the power of which modern anarchy prevents them from appreciating as they should.

Thus, my philosophical endeavors have been carried on and completed not only in the face of material difficulties, as you know, but also in the midst of more painful and absorbing disturbances, the result of an almost constant civil war of the most intimate kind, the confrontation in the home.
The event which has just taken place makes me hope that from now on, even if I lack the happiness at home for which I was made but which I had to give up a long time ago, I shall at least have the sad peace of my loneliness that now completely envelops me.
At yet another crisis in the relationship, Caroline found an apartment for herself in the 9th arrondissement and moved there on 5 August 1842.
This time the separation proved final. 
She left Comte just after the completion of his Cours de philosophie positive.
Caroline recognized that the problems with the marriage were due to her insistence on equality. She wrote,
I have always been devoted to you, but I was not at all submissive. If there had been less real devotion and more submission, things would have been better between us. Many times you were basically right, but you asked me to yield in the name of your authority, and I stood up to you when I should have submitted. Really, I did not know how to be submissive, but even so, I did love you. You know that very well. ... My great crime was to see in you a husband, not a master. I know very well that you are superior to me in many respects, and besides, this comparison has always seemed to me . . . most absurd. We did not do the same things. 
Comte wrote to John Stuart Mill on 24 August 1842 to pour out his troubles,
Our personal friendship (...) causes me not to wait any longer to give you an important piece of personal news. A fundamental change, more favorable than unfavorable, has occurred in my household since my last letter. Madame Comte has left me voluntarily and probably irrevocably. For seventeen years I have been married, as a result of an unfortunate love to a woman of rare moral and intellectual qualities, but brought up under blameworthy principles and with a false notion of the essential function that her sex must play in the human economy. Her total lack of affection for me has never made it possible for me to overlook either her resistance to my authority or her despotic character. There have been none of the compensations of a loving disposition, the only special quality in which women are irreplaceable, and the power of which modern anarchy prevents them from appreciating as they should.
Thus, my philosophical endeavors have been carried on and completed not only in the face of material difficulties, as you know, but also in the midst of more painful and absorbing disturbances, the result of an almost constant civil war of the most intimate kind, the confrontation in the home. The event which has just taken place makes me hope that from now on, even if I lack the happiness at home for which I was made but which I had to give up a long time ago, I shall at least have the sad peace of my loneliness that now completely envelops me.
Caroline Massin