Shankara considered Sāṃkhya philosophy his "chief opponent" (pradhāna malla) because, despite its intellectual sophistication and concern for liberation (mokṣa), it presented a fundamentally different metaphysical system that directly challenged Advaita Vedānta’s core tenets. Sāṃkhya's dualism between an independent, unconscious primordial matter (Prakriti) and multiple conscious selves (Puruṣas) stood in stark contrast to Advaita's radical non-dualism, where Brahman alone is ultimately real. Sāṃkhya offered a robust, rational system that needed to be systematically dismantled to establish Advaita's supremacy.

Shankara's main arguments against Sāṃkhya primarily focused on its theory of causation:

1. Prakriti as an Unconscious Cause (Achetanakāraṇatva-nirākaraṇa):
   Sāṃkhya posits an unconscious, unintelligent Prakriti as the sole material cause of the universe. Shankara vehemently argued that an unconscious entity cannot logically produce an ordered, purposeful, and complex world. The universe exhibits intelligence and design, which, according to Shankara, can only originate from an intelligent, conscious cause – Brahman. An unguided, insentient principle like Prakriti would lead to chaos, not a cosmos. He stressed that a cause must possess the intelligence reflected in its effect.

2. Inexplicability of Conjunction (Sambandhānupapatti):
   Sāṃkhya asserts that Puruṣa (consciousness) and Prakriti (matter) are eternally distinct, independent, and entirely different. Shankara questioned how these two fundamentally disparate entities could ever come into contact or association, which Sāṃkhya requires for creation and the experience of bondage. An unconscious Prakriti cannot move itself, and a pure, detached Puruṣa has no inherent reason or mechanism to interact with it. If their conjunction is inexplicable, then the entire Sāṃkhya explanation of creation and experience falters.

3. Undermining the Goal of Liberation:
   Shankara also argued that if Puruṣa is eternally pure and detached, as Sāṃkhya claims, then there is no real bondage in the first place. This makes the Sāṃkhya goal of liberation (kaivalya) problematic. If Puruṣa is never truly affected by Prakriti, then the whole cycle of suffering and the need for release becomes illusory even within Sāṃkhya's own framework, albeit a different kind of illusion than Advaita's.

By dismantling Sāṃkhya's dualistic metaphysics and its concept of an unconscious primary cause, Shankara aimed to prove that Brahman, as the sole, intelligent, and conscious material and efficient cause, is the only logically coherent explanation for the universe, solidifying the foundation for Advaita's non-dual reality.