Fortunately, reason kicked in(,) and I stopped doing it.
I read somewhere that you should always add a comma if the sentence after the "and" is a complete sentence. This seems to be the case in my example.
However, I also see the no-comma version on Google Books:
[...] but reason kicked in and I turned the thought down.
[...] The voice of reason kicked in and I was forced to face the truth and to undertake some real, heartfelt, sincere, and honest examinations.
Maybe both versions are correct?