"From sublimation of this union comes the peaceful flow of unbroken unitive cognition."
When you think of purity of thought, what comes to mind? When we are children, most of what we think is "pure" come from external conditioning. In the Judeo-Christian tradition, we have the ten commandments. In Islam, the Five Pillars represent a form or purity. Earlier in the Sutras, I wrote about the Yamas and Niyamas, which are the do's and don't of Yoga. Those are all great for beginners, but we are now on book three. Time to throw those concepts away!
"What, why would I do that" you ask? Everything a Yogi does, EVERYTHING, is a means to an end, that end being Moksha. The natural state of the universal cycle runs in three phases: creation, preservation and destruction. The Yogi's worship the deity Kali, the name given to the dissolution principle. Yoga is ultimately about taking things away, not adding things. If this sounds like a contradiction, it is. It's the only way to express something in linear thought that exists outside of time. So we start with a basic framework, build ourselves up within it, then tear it down again to approach the same subject with a larger framework.
This Sutra is speaking about the state of consciousness when thought is no longer initiated by external stimuli. It's a hard feeling to describe, but when you feel it, you will know it. This is where the guidance of a Guru or community of fellow practitioners can help. Now you are running on pure intuitive experience balanced with untainted logic. Just realize that when you reach a new level of understanding, you are going from a smaller construct into a larger one. Constructs need to be consistently dissolved until they no longer exist. So like Smashing Pumpkins lyric from Bullet with Butterfly Wings said "Despite all my rage, I'm still just a rat in a cage!", you move from a smaller cage into a larger cage. Don't worry, at some point, you will leave the zoo.