In Scientology universe, it is always the irrational part of the mind that causes troubles. However, Scientology is not materialist, so "mind" doesn't necessarily imply a material brain. It could be a mind of an invisible alien spirit attached to your body.

In Scientology universe (but this is what you only learn at the highest levels, when Hubbard already ran out of anything remotely sane to teach), there are many alien spirits attached to our bodies... because they are brainwashed by giant space brainwashing facilities on the Earth orbit, installed billions of years ago by an evil space emperor Xenu... and the alien spirits irrationally believe that they are identical to us. Then, using the super secret and super expensive Scientology techniques, you can connect telepathically to them, provide them psychotherapy, teach them some basic rationality, and they will understand their errors and leave your body.

So, yeah, on some level it is batshit insane... however, if you could accept the premises of the Scientology universe, where immaterial spirits exist with immaterial minds, and can behave irrationally... then the Scientology exercises kinda would be the rational thing to do.